Query 009173
Match_columns 541
No_of_seqs 278 out of 1847
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 21:18:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009173.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009173hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2192 PolyC-binding hnRNP-K 100.0 8.7E-36 1.9E-40 288.1 23.7 324 182-539 44-385 (390)
2 KOG1676 K-homology type RNA bi 100.0 7.3E-36 1.6E-40 317.0 21.2 283 146-537 96-388 (600)
3 KOG2190 PolyC-binding proteins 100.0 2.3E-32 5E-37 294.0 27.9 331 183-538 40-409 (485)
4 KOG1676 K-homology type RNA bi 100.0 3.3E-31 7.1E-36 281.7 21.3 247 184-538 52-300 (600)
5 KOG2193 IGF-II mRNA-binding pr 100.0 1.1E-31 2.5E-36 273.0 15.9 287 180-540 193-483 (584)
6 KOG2191 RNA-binding protein NO 99.9 1.9E-26 4.1E-31 229.4 19.9 267 185-538 38-315 (402)
7 KOG2193 IGF-II mRNA-binding pr 99.9 4.4E-25 9.6E-30 225.1 12.6 240 183-537 277-563 (584)
8 KOG2191 RNA-binding protein NO 99.9 1.6E-21 3.4E-26 194.5 16.6 164 277-540 38-206 (402)
9 KOG2190 PolyC-binding proteins 99.7 1.9E-16 4.1E-21 171.2 15.4 158 277-539 42-209 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.6 9.7E-16 2.1E-20 149.3 12.2 217 118-351 61-384 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.6 1.2E-15 2.7E-20 144.8 10.6 136 282-536 2-149 (172)
12 PRK13763 putative RNA-processi 99.6 2.3E-14 5E-19 137.1 12.7 149 278-536 3-155 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.6 9.7E-15 2.1E-19 138.7 10.0 138 190-352 2-152 (172)
14 PRK13763 putative RNA-processi 99.5 9.5E-14 2.1E-18 132.8 10.6 141 186-351 3-157 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 2.9E-13 6.3E-18 108.1 7.0 63 471-533 2-65 (65)
16 KOG2279 Kinase anchor protein 99.4 4E-12 8.6E-17 135.1 12.3 292 182-534 64-364 (608)
17 cd02396 PCBP_like_KH K homolog 99.3 4.6E-12 1E-16 101.1 5.9 65 279-346 1-65 (65)
18 cd02394 vigilin_like_KH K homo 99.2 1E-11 2.2E-16 98.0 5.9 61 471-533 2-62 (62)
19 PF00013 KH_1: KH domain syndr 99.2 7.2E-12 1.6E-16 98.1 4.9 60 470-532 1-60 (60)
20 cd00105 KH-I K homology RNA-bi 99.2 2.3E-11 5E-16 95.9 7.5 63 471-533 2-64 (64)
21 cd02393 PNPase_KH Polynucleoti 99.2 5.7E-11 1.2E-15 93.7 7.1 58 470-533 3-61 (61)
22 PF00013 KH_1: KH domain syndr 99.0 2E-10 4.2E-15 90.0 4.2 60 279-345 1-60 (60)
23 cd02394 vigilin_like_KH K homo 99.0 3.6E-10 7.9E-15 89.0 5.5 60 280-345 2-61 (62)
24 cd02393 PNPase_KH Polynucleoti 99.0 5.3E-10 1.1E-14 88.2 6.2 58 278-345 2-60 (61)
25 cd00105 KH-I K homology RNA-bi 98.9 2.7E-09 5.9E-14 84.0 6.2 53 188-240 2-54 (64)
26 PF13014 KH_3: KH domain 98.9 3E-09 6.5E-14 77.8 5.3 42 196-237 1-43 (43)
27 smart00322 KH K homology RNA-b 98.9 1.3E-08 2.7E-13 80.1 8.9 66 469-536 3-68 (69)
28 PF13014 KH_3: KH domain 98.9 3.9E-09 8.5E-14 77.2 5.3 42 479-520 1-43 (43)
29 KOG2279 Kinase anchor protein 98.7 1.6E-08 3.5E-13 108.0 4.1 146 275-539 65-210 (608)
30 smart00322 KH K homology RNA-b 98.6 1.1E-07 2.4E-12 74.6 7.4 66 278-349 3-68 (69)
31 COG1094 Predicted RNA-binding 98.6 2.3E-07 5E-12 88.5 10.5 142 186-350 8-163 (194)
32 KOG2208 Vigilin [Lipid transpo 98.6 4.4E-07 9.6E-12 104.0 12.5 233 183-536 198-486 (753)
33 COG1094 Predicted RNA-binding 98.5 4.4E-07 9.5E-12 86.6 10.1 146 279-538 9-164 (194)
34 cd02395 SF1_like-KH Splicing f 98.2 4.8E-06 1E-10 74.6 7.0 61 478-538 15-95 (120)
35 KOG2208 Vigilin [Lipid transpo 98.1 5.4E-06 1.2E-10 95.2 8.2 142 184-350 345-487 (753)
36 cd02395 SF1_like-KH Splicing f 98.1 7E-06 1.5E-10 73.5 5.8 66 286-351 14-95 (120)
37 KOG2113 Predicted RNA binding 98.0 8.3E-06 1.8E-10 82.2 6.1 150 275-529 23-173 (394)
38 KOG2113 Predicted RNA binding 97.9 1E-05 2.2E-10 81.6 3.4 146 184-348 24-180 (394)
39 PRK08406 transcription elongat 97.8 2.1E-05 4.6E-10 72.4 5.0 102 187-313 33-134 (140)
40 TIGR02696 pppGpp_PNP guanosine 97.5 0.00028 6E-09 80.1 8.5 66 276-351 576-642 (719)
41 TIGR02696 pppGpp_PNP guanosine 97.5 0.00027 5.8E-09 80.2 7.8 62 470-537 579-641 (719)
42 PRK08406 transcription elongat 97.4 0.00025 5.4E-09 65.3 6.2 37 469-505 99-135 (140)
43 KOG0119 Splicing factor 1/bran 97.4 0.00076 1.7E-08 72.2 9.2 75 277-351 137-230 (554)
44 TIGR01952 nusA_arch NusA famil 97.3 0.00037 8.1E-09 64.2 4.9 102 187-313 34-135 (141)
45 TIGR03591 polynuc_phos polyrib 97.1 0.001 2.2E-08 76.3 7.2 65 277-351 550-615 (684)
46 TIGR03591 polynuc_phos polyrib 97.0 0.0011 2.5E-08 75.9 6.6 63 469-537 551-614 (684)
47 TIGR01952 nusA_arch NusA famil 96.9 0.0017 3.7E-08 59.8 5.6 37 469-505 100-136 (141)
48 KOG0336 ATP-dependent RNA heli 96.9 0.0019 4.2E-08 68.1 6.4 66 469-537 47-112 (629)
49 TIGR03319 YmdA_YtgF conserved 96.7 0.0039 8.5E-08 69.2 7.7 68 468-540 203-272 (514)
50 COG0195 NusA Transcription elo 96.7 0.0044 9.6E-08 59.9 7.1 102 187-314 77-178 (190)
51 PRK00106 hypothetical protein; 96.6 0.005 1.1E-07 68.3 8.0 68 468-540 224-293 (535)
52 PRK12704 phosphodiesterase; Pr 96.5 0.0069 1.5E-07 67.4 7.9 68 468-540 209-278 (520)
53 KOG0336 ATP-dependent RNA heli 96.5 0.0029 6.3E-08 66.8 4.5 68 275-349 44-111 (629)
54 KOG1588 RNA-binding protein Sa 96.4 0.0032 6.9E-08 63.0 4.3 41 183-223 89-135 (259)
55 cd02134 NusA_KH NusA_K homolog 96.4 0.0051 1.1E-07 48.4 4.5 36 186-221 25-60 (61)
56 PLN00207 polyribonucleotide nu 96.4 0.0048 1E-07 71.8 5.9 66 276-351 683-750 (891)
57 cd02134 NusA_KH NusA_K homolog 96.4 0.005 1.1E-07 48.5 4.2 36 469-504 25-60 (61)
58 KOG0119 Splicing factor 1/bran 96.3 0.0077 1.7E-07 64.7 6.8 61 478-538 153-230 (554)
59 PLN00207 polyribonucleotide nu 96.0 0.0059 1.3E-07 71.1 4.5 63 469-537 685-749 (891)
60 KOG2814 Transcription coactiva 96.0 0.0093 2E-07 61.4 5.2 68 469-538 57-125 (345)
61 COG1185 Pnp Polyribonucleotide 95.9 0.011 2.3E-07 66.3 5.7 64 469-538 552-616 (692)
62 COG1185 Pnp Polyribonucleotide 95.9 0.019 4.1E-07 64.5 7.2 66 278-353 552-618 (692)
63 PRK04163 exosome complex RNA-b 95.7 0.021 4.5E-07 57.2 6.2 60 471-536 147-207 (235)
64 PRK11824 polynucleotide phosph 95.6 0.015 3.1E-07 67.1 5.1 64 278-351 554-618 (693)
65 PRK00468 hypothetical protein; 95.4 0.018 3.9E-07 47.3 3.7 34 182-215 26-59 (75)
66 TIGR01953 NusA transcription t 95.3 0.042 9E-07 58.0 7.1 94 196-315 244-338 (341)
67 PRK12328 nusA transcription el 95.2 0.031 6.8E-07 59.2 5.9 92 196-314 252-344 (374)
68 COG5176 MSL5 Splicing factor ( 95.2 0.03 6.5E-07 54.1 5.0 37 469-505 148-190 (269)
69 KOG2814 Transcription coactiva 95.2 0.02 4.4E-07 58.9 4.2 69 278-352 57-126 (345)
70 PRK04163 exosome complex RNA-b 95.1 0.039 8.4E-07 55.3 5.8 64 280-353 147-211 (235)
71 KOG1588 RNA-binding protein Sa 95.1 0.029 6.3E-07 56.2 4.8 38 468-505 91-134 (259)
72 KOG4369 RTK signaling protein 95.1 0.0079 1.7E-07 69.9 0.9 70 467-536 1338-1408(2131)
73 PRK12327 nusA transcription el 95.0 0.051 1.1E-06 57.7 6.7 94 196-315 246-340 (362)
74 PRK02821 hypothetical protein; 95.0 0.024 5.3E-07 46.8 3.4 36 182-217 27-62 (77)
75 PRK09202 nusA transcription el 94.8 0.052 1.1E-06 59.6 6.4 93 196-315 246-339 (470)
76 PF14611 SLS: Mitochondrial in 94.7 0.83 1.8E-05 44.6 14.1 63 279-350 27-89 (210)
77 PRK12329 nusA transcription el 94.7 0.048 1E-06 58.8 5.6 93 196-314 278-371 (449)
78 PRK12705 hypothetical protein; 94.7 0.039 8.4E-07 61.0 5.1 68 468-540 197-266 (508)
79 COG0195 NusA Transcription elo 94.7 0.049 1.1E-06 52.7 5.1 37 470-506 143-179 (190)
80 TIGR03319 YmdA_YtgF conserved 94.6 0.089 1.9E-06 58.6 7.8 64 279-351 205-270 (514)
81 PRK12704 phosphodiesterase; Pr 94.6 0.083 1.8E-06 58.9 7.5 64 279-351 211-276 (520)
82 PRK11824 polynucleotide phosph 94.4 0.03 6.5E-07 64.5 3.6 62 470-537 555-617 (693)
83 PRK00106 hypothetical protein; 94.4 0.12 2.6E-06 57.5 8.0 64 279-351 226-291 (535)
84 PRK00468 hypothetical protein; 94.3 0.037 8E-07 45.5 2.8 32 275-306 27-58 (75)
85 COG1837 Predicted RNA-binding 94.3 0.051 1.1E-06 44.7 3.6 33 183-215 27-59 (76)
86 PRK01064 hypothetical protein; 94.0 0.056 1.2E-06 44.8 3.4 34 182-215 26-59 (78)
87 COG1837 Predicted RNA-binding 93.9 0.049 1.1E-06 44.8 2.8 32 275-306 27-58 (76)
88 COG5176 MSL5 Splicing factor ( 93.8 0.16 3.5E-06 49.1 6.6 40 275-314 145-190 (269)
89 PF14611 SLS: Mitochondrial in 93.8 1 2.2E-05 44.0 12.5 126 190-350 30-164 (210)
90 PRK02821 hypothetical protein; 93.0 0.083 1.8E-06 43.7 2.7 32 469-500 31-62 (77)
91 PRK01064 hypothetical protein; 92.3 0.12 2.7E-06 42.8 2.9 32 275-306 27-58 (78)
92 PRK09202 nusA transcription el 91.8 0.29 6.2E-06 53.9 5.9 37 470-506 303-339 (470)
93 PF13083 KH_4: KH domain; PDB: 91.2 0.12 2.6E-06 42.0 1.7 35 183-217 26-60 (73)
94 KOG3273 Predicted RNA-binding 90.8 0.2 4.3E-06 48.3 3.0 54 286-350 177-230 (252)
95 cd02409 KH-II KH-II (K homolo 90.0 0.45 9.9E-06 36.9 4.1 35 185-219 24-58 (68)
96 PF13184 KH_5: NusA-like KH do 88.8 0.33 7.1E-06 39.3 2.4 35 188-222 5-45 (69)
97 PRK12705 hypothetical protein; 88.7 0.72 1.6E-05 51.2 5.8 62 280-350 200-263 (508)
98 KOG4369 RTK signaling protein 88.0 0.53 1.1E-05 55.6 4.2 71 279-352 1341-1411(2131)
99 cd02409 KH-II KH-II (K homolo 86.1 1.3 2.7E-05 34.4 4.3 34 469-502 25-58 (68)
100 PF13083 KH_4: KH domain; PDB: 85.9 0.37 7.9E-06 39.0 1.1 33 277-309 28-60 (73)
101 PF07650 KH_2: KH domain syndr 85.3 0.46 9.9E-06 38.9 1.5 35 186-220 25-59 (78)
102 cd02414 jag_KH jag_K homology 84.9 0.88 1.9E-05 37.3 3.0 34 187-220 25-58 (77)
103 PF13184 KH_5: NusA-like KH do 84.3 0.86 1.9E-05 36.8 2.6 36 470-505 4-45 (69)
104 KOG3273 Predicted RNA-binding 83.1 0.82 1.8E-05 44.2 2.3 56 477-539 177-232 (252)
105 PF07650 KH_2: KH domain syndr 83.1 0.49 1.1E-05 38.7 0.7 34 469-502 25-58 (78)
106 KOG1067 Predicted RNA-binding 82.7 4.8 0.0001 44.7 8.2 66 275-351 594-660 (760)
107 COG1855 ATPase (PilT family) [ 79.9 1.3 2.8E-05 48.2 2.6 37 187-223 487-523 (604)
108 cd02413 40S_S3_KH K homology R 79.8 2 4.3E-05 35.8 3.2 36 187-222 31-66 (81)
109 KOG2874 rRNA processing protei 79.5 3.5 7.6E-05 41.9 5.4 51 481-538 161-211 (356)
110 PRK06418 transcription elongat 79.2 2.7 5.9E-05 39.8 4.4 35 187-222 62-96 (166)
111 TIGR01953 NusA transcription t 78.3 2 4.2E-05 45.5 3.4 37 469-505 301-337 (341)
112 cd02410 archeal_CPSF_KH The ar 78.1 6.3 0.00014 36.5 6.2 92 201-315 21-113 (145)
113 cd02414 jag_KH jag_K homology 77.7 2.5 5.3E-05 34.7 3.2 34 470-503 25-58 (77)
114 PRK12328 nusA transcription el 76.5 2.5 5.4E-05 45.1 3.6 37 469-505 308-344 (374)
115 PRK13764 ATPase; Provisional 76.3 2.2 4.8E-05 48.4 3.4 39 467-505 479-517 (602)
116 COG1097 RRP4 RNA-binding prote 76.3 5.5 0.00012 39.8 5.7 36 471-506 148-183 (239)
117 KOG1067 Predicted RNA-binding 76.2 3 6.6E-05 46.2 4.2 64 469-539 597-661 (760)
118 PRK13764 ATPase; Provisional 76.1 2.1 4.5E-05 48.7 3.0 38 186-223 481-518 (602)
119 COG1855 ATPase (PilT family) [ 74.9 1.9 4.2E-05 46.9 2.3 37 469-505 486-522 (604)
120 KOG2874 rRNA processing protei 74.3 4.4 9.4E-05 41.2 4.4 51 290-351 161-211 (356)
121 cd02413 40S_S3_KH K homology R 74.1 3.9 8.4E-05 34.1 3.5 36 469-504 30-65 (81)
122 COG1097 RRP4 RNA-binding prote 74.1 5.7 0.00012 39.8 5.2 59 280-348 148-207 (239)
123 cd02412 30S_S3_KH K homology R 72.7 3.5 7.6E-05 36.3 3.0 31 187-217 62-92 (109)
124 PRK12327 nusA transcription el 72.5 3.7 7.9E-05 43.8 3.7 37 469-505 303-339 (362)
125 cd02410 archeal_CPSF_KH The ar 71.2 5.4 0.00012 36.9 4.0 38 469-506 76-113 (145)
126 cd02411 archeal_30S_S3_KH K ho 68.9 5.3 0.00012 33.4 3.2 28 188-215 40-67 (85)
127 PRK06418 transcription elongat 66.4 7 0.00015 37.1 3.8 36 470-506 62-97 (166)
128 PRK12329 nusA transcription el 66.1 5 0.00011 43.7 3.1 38 469-506 335-372 (449)
129 COG0092 RpsC Ribosomal protein 65.6 5.3 0.00012 39.8 2.9 32 185-216 50-81 (233)
130 COG1782 Predicted metal-depend 64.0 11 0.00025 41.6 5.2 94 199-316 42-137 (637)
131 cd02411 archeal_30S_S3_KH K ho 62.7 8 0.00017 32.3 3.1 28 471-498 40-67 (85)
132 cd02412 30S_S3_KH K homology R 62.6 6.7 0.00015 34.5 2.7 29 471-499 63-91 (109)
133 COG0092 RpsC Ribosomal protein 58.1 9.1 0.0002 38.2 3.0 35 470-504 52-91 (233)
134 TIGR03675 arCOG00543 arCOG0054 50.7 30 0.00065 39.8 6.1 94 200-316 37-131 (630)
135 TIGR00436 era GTP-binding prot 44.7 23 0.0005 35.8 3.6 30 469-498 221-251 (270)
136 COG5166 Uncharacterized conser 43.0 25 0.00054 38.9 3.7 66 187-252 450-518 (657)
137 COG1782 Predicted metal-depend 41.0 28 0.00061 38.6 3.7 38 469-506 99-136 (637)
138 COG5166 Uncharacterized conser 41.0 15 0.00032 40.6 1.6 129 198-352 392-525 (657)
139 COG1702 PhoH Phosphate starvat 41.0 63 0.0014 34.3 6.1 50 477-533 23-72 (348)
140 TIGR03675 arCOG00543 arCOG0054 41.0 29 0.00063 39.9 4.1 38 469-506 93-130 (630)
141 TIGR00436 era GTP-binding prot 40.9 18 0.0004 36.5 2.2 30 186-215 221-251 (270)
142 PRK15494 era GTPase Era; Provi 38.1 32 0.0007 36.2 3.6 37 469-505 273-318 (339)
143 PRK00089 era GTPase Era; Revie 37.9 34 0.00073 34.8 3.7 37 469-505 226-271 (292)
144 TIGR01008 rpsC_E_A ribosomal p 37.6 32 0.0007 33.5 3.2 31 187-217 39-69 (195)
145 CHL00048 rps3 ribosomal protei 37.0 33 0.00071 34.0 3.2 30 187-216 67-96 (214)
146 PTZ00084 40S ribosomal protein 36.3 34 0.00074 34.0 3.2 33 187-219 45-77 (220)
147 PRK04191 rps3p 30S ribosomal p 36.2 34 0.00074 33.6 3.2 31 188-218 42-72 (207)
148 PRK00089 era GTPase Era; Revie 36.1 24 0.00051 36.0 2.2 37 186-222 226-271 (292)
149 COG1159 Era GTPase [General fu 35.3 40 0.00086 35.0 3.6 36 469-504 229-273 (298)
150 PRK15494 era GTPase Era; Provi 32.1 30 0.00064 36.5 2.2 36 186-221 273-317 (339)
151 PRK04191 rps3p 30S ribosomal p 31.5 44 0.00095 32.9 3.1 29 471-499 42-70 (207)
152 COG1159 Era GTPase [General fu 31.0 34 0.00074 35.5 2.3 37 185-221 228-273 (298)
153 TIGR01008 rpsC_E_A ribosomal p 30.7 50 0.0011 32.3 3.3 29 470-498 39-67 (195)
154 COG1847 Jag Predicted RNA-bind 30.1 38 0.00082 33.3 2.4 35 187-221 92-126 (208)
155 PTZ00084 40S ribosomal protein 28.5 53 0.0011 32.7 3.1 29 470-498 45-73 (220)
156 PRK13916 plasmid segregation p 27.4 36 0.00078 28.6 1.4 33 59-95 16-48 (97)
157 CHL00048 rps3 ribosomal protei 27.4 56 0.0012 32.3 3.1 29 470-498 67-95 (214)
158 KOG1423 Ras-like GTPase ERA [C 27.0 55 0.0012 34.4 3.0 33 184-216 326-359 (379)
159 COG1847 Jag Predicted RNA-bind 26.4 45 0.00097 32.8 2.1 35 279-313 92-126 (208)
160 KOG1423 Ras-like GTPase ERA [C 26.4 60 0.0013 34.1 3.1 32 468-499 327-359 (379)
161 PF02080 TrkA_C: TrkA-C domain 24.1 1.6E+02 0.0034 22.8 4.6 45 488-532 14-70 (71)
162 PF02749 QRPTase_N: Quinolinat 23.7 2.2E+02 0.0048 23.7 5.6 51 487-537 32-85 (88)
163 TIGR01009 rpsC_bact ribosomal 23.2 77 0.0017 31.3 3.2 29 188-216 64-92 (211)
No 1
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=8.7e-36 Score=288.08 Aligned_cols=324 Identities=26% Similarity=0.402 Sum_probs=213.8
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (541)
Q Consensus 182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e 261 (541)
....+.++||+.++.+|+||||+|++||+|+.+++|.|+|++ .+.++|+++|+...+ .+..|+.+++.
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd--s~~peri~tisad~~----------ti~~ilk~iip 111 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILTISADIE----------TIGEILKKIIP 111 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccC--CCCCceeEEEeccHH----------HHHHHHHHHhh
Confidence 455699999999999999999999999999999999999986 567999999998644 45555555443
Q ss_pred cccccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHH
Q 009173 262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341 (541)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A 341 (541)
.. +.++ .....+.++|+|..+++|.|||++|++||++++++.|+.+|..+- |..++||+|.|.|.+..|..+
T Consensus 112 ~l-ee~f----~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c---~p~stdrv~l~~g~~k~v~~~ 183 (390)
T KOG2192|consen 112 TL-EEGF----QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTEC---CPHSTDRVVLIGGKPKRVVEC 183 (390)
T ss_pred hh-hhCC----CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhcc---CCCCcceEEEecCCcchHHHH
Confidence 21 1111 234568899999999999999999999999999999999998664 445999999999999999999
Q ss_pred HHHHHHHhhccccCCCcccccccC-CC----Cc---cccCCCCCCCCCCCcccccccccc---CCCCCCCC----CccCC
Q 009173 342 VYNVTGRLRDNHFSGTLNTARTRS-TS----SV---LTETSPYSRLKDPASFGVHSSVAV---SHDFSQPP----LTQGM 406 (541)
Q Consensus 342 ~~lI~~~l~e~~~~~~~~~~~~~~-~~----~~---~~~~~p~~~~~~p~~~~~~~~~g~---~~~~~r~~----~~~~~ 406 (541)
++.|++.|.|.+.++...++.... ++ .. +-...|..+...|-+-+..++.+. -...+|.. -..+|
T Consensus 184 i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~ 263 (390)
T KOG2192|consen 184 IKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGM 263 (390)
T ss_pred HHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccc
Confidence 999999999988776544433221 11 00 001111111100000000000000 00000100 00022
Q ss_pred CccCCCCCCCCCC---CCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccce
Q 009173 407 DHLGLSHSLDCPS---SPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSV 483 (541)
Q Consensus 407 ~~~~~~~~~~~p~---~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~I 483 (541)
..+.....|..+. ++..|. .+|.|.+.... ..+.-+....+..... ..+|.+|+||.++-|.|
T Consensus 264 vdFs~detw~saidtw~~Sewq----maYePQgGs~y-------dysyAG~~GsYGdlGG---PitTaQvtip~dlggsi 329 (390)
T KOG2192|consen 264 VDFSADETWPSAIDTWSPSEWQ----MAYEPQGGSGY-------DYSYAGGYGSYGDLGG---PITTAQVTIPKDLGGSI 329 (390)
T ss_pred ccccccccCCCcCCCcCccccc----cccCCCCCCCC-------CccccccccccCCCCC---ceeeeeEecccccCcce
Confidence 2222222222111 112221 11111111000 0000000000000001 24789999999999999
Q ss_pred eeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173 484 YGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG 539 (541)
Q Consensus 484 IGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~ 539 (541)
|||||.+|++|++++||.|+|++|..++.+|+|+|+||.+|++.||+|+|+.+..+
T Consensus 330 igkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 330 IGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred ecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999753
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=7.3e-36 Score=316.98 Aligned_cols=283 Identities=22% Similarity=0.314 Sum_probs=219.4
Q ss_pred CCcccccCCCCcccccccccCCCccccccc--c-hhhcccCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEec
Q 009173 146 RNSVLTTAPSSSISYVSAVRPLSLESDRVA--T-LDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG 222 (541)
Q Consensus 146 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~ 222 (541)
..+|.+.+.|...++..+++.+.....+-- . .........++..|+||++.+|+||||+|++||+||+++||++.+-
T Consensus 96 ~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~i 175 (600)
T KOG1676|consen 96 IGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILV 175 (600)
T ss_pred cccccccccCCcccHHHHHHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEE
Confidence 356777788877777777777765433321 0 1122335668999999999999999999999999999999999977
Q ss_pred CCC--CCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc---cCCCCCCCCCceeEEEEEeccccccccccccc
Q 009173 223 ATM--PECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE---KGLDFSSNKGLLVNARLVVASNQVGCLLGKGG 297 (541)
Q Consensus 223 ~~~--~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~---~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG 297 (541)
... .....+.+.|+|.++. +..|..++.+.|.|..-+ .+.+++.......+.++.||.+.||.||||+|
T Consensus 176 qd~~~~~~~~KplritGdp~~------ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgG 249 (600)
T KOG1676|consen 176 QDGSIATGADKPLRITGDPDK------VEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGG 249 (600)
T ss_pred ecCCcCCCCCCceeecCCHHH------HHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCc
Confidence 542 2237789999998774 667777777655542211 11223333455568999999999999999999
Q ss_pred chhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCC
Q 009173 298 TIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYS 377 (541)
Q Consensus 298 ~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~ 377 (541)
++||+|+.+||++|+|..|..|. +.||.+.|.|+.+.|+.|.++|.++|.+.....
T Consensus 250 E~IKklq~etG~KIQfkpDd~p~---speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~--------------------- 305 (600)
T KOG1676|consen 250 EMIKKLQNETGAKIQFKPDDDPS---SPERPAQIIGTVDQIEHAAELINEIIAEAEAGA--------------------- 305 (600)
T ss_pred hHHHHHhhccCceeEeecCCCCC---CccceeeeecCHHHHHHHHHHHHHHHHHHhccC---------------------
Confidence 99999999999999999887774 889999999999999999999999997532000
Q ss_pred CCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCccc
Q 009173 378 RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLEL 457 (541)
Q Consensus 378 ~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~ 457 (541)
+ ++|..|.+ +
T Consensus 306 ---------------------------~------------------------------------~~~~~G~P---~---- 315 (600)
T KOG1676|consen 306 ---------------------------G------------------------------------GGMGGGAP---G---- 315 (600)
T ss_pred ---------------------------C------------------------------------CCcCCCCc---c----
Confidence 0 00112222 0
Q ss_pred CCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC--CCCCCCccEEEEEeCHHHHHHHHHHHHHH
Q 009173 458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE--PRLGSTDRIVVISGTPDETQAAQSLLQAF 535 (541)
Q Consensus 458 ~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~--p~~~s~~RiItIsGtpeqV~~Aq~LI~~~ 535 (541)
....+++.||.++||+||||||+|||.|.++|||++.+.. |..+..++.|+|+|++.||+.|++||+.+
T Consensus 316 ---------~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~k 386 (600)
T KOG1676|consen 316 ---------LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDK 386 (600)
T ss_pred ---------ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHH
Confidence 0127899999999999999999999999999999999984 44566899999999999999999999999
Q ss_pred Hh
Q 009173 536 IL 537 (541)
Q Consensus 536 I~ 537 (541)
+-
T Consensus 387 vg 388 (600)
T KOG1676|consen 387 VG 388 (600)
T ss_pred hc
Confidence 84
No 3
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.3e-32 Score=294.04 Aligned_cols=331 Identities=27% Similarity=0.426 Sum_probs=213.8
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhc
Q 009173 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG 262 (541)
Q Consensus 183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~ 262 (541)
....++||||+.+.+|.||||+|.+||+|+.+|+++|+|.+..++|.||+++|+|.... ...+++++|+.++++.++..
T Consensus 40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-~~~~~~~~al~ka~~~iv~~ 118 (485)
T KOG2190|consen 40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-LNLSPATDALFKAFDMIVFK 118 (485)
T ss_pred CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-ccCCchHHHHHHHHHHHhhc
Confidence 34456999999999999999999999999999999999999999999999999995322 26677899999999887763
Q ss_pred cc---ccCCCCC-CCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHH
Q 009173 263 TS---EKGLDFS-SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKV 338 (541)
Q Consensus 263 ~~---~~g~~~~-~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V 338 (541)
.. ....+.+ ......++++|+||.+++|+||||+|+.||+|+++|||+|+|.++.+|. .++|.|+|.|.+++|
T Consensus 119 ~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av 195 (485)
T KOG2190|consen 119 LEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAV 195 (485)
T ss_pred ccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHH
Confidence 11 1111222 1122368999999999999999999999999999999999999889998 578899999999999
Q ss_pred HHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCCC------------------------CC---CC-Cccccccc
Q 009173 339 KDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSR------------------------LK---DP-ASFGVHSS 390 (541)
Q Consensus 339 ~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~------------------------~~---~p-~~~~~~~~ 390 (541)
.+|+..|..+|+++.-.. . ..+....||.+ .. +. ..+..+..
T Consensus 196 ~~al~~Is~~L~~~~~~~---~-------~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~ 265 (485)
T KOG2190|consen 196 KKALVQISSRLLENPPRS---P-------PPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSD 265 (485)
T ss_pred HHHHHHHHHHHHhcCCcC---C-------CCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchh
Confidence 999999999999864110 0 00111122211 00 00 00000000
Q ss_pred c--cc---CCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCccc
Q 009173 391 V--AV---SHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAI 465 (541)
Q Consensus 391 ~--g~---~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~ 465 (541)
. ++ .....+.- -+..+. ....+...+ ......+.... +...-...-........... ......+
T Consensus 266 ~~~~v~g~~~~~i~~l-~~~~~~-~i~v~~~~~--~~~i~~s~~e~--~~~~~s~a~~a~~~~~~~~~----~~~~~~~- 334 (485)
T KOG2190|consen 266 KVGSVIGKGGLVIRAL-RNETGA-SISVGDSRT--DRIVTISAREN--PEDRYSMAQEALLLVQPRIS----ENAGDDL- 334 (485)
T ss_pred hceeeecCCCccchhh-hhhcCC-ceEeccccC--cceeeeccccC--cccccccchhhhhhcccccc----ccccccc-
Confidence 0 00 00000000 000000 000000000 00000000000 00000000000000000000 0000111
Q ss_pred ccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCC--CCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173 466 VTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL--GSTDRIVVISGTPDETQAAQSLLQAFILT 538 (541)
Q Consensus 466 ~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~--~s~~RiItIsGtpeqV~~Aq~LI~~~I~~ 538 (541)
....+.++.||.+++|+||||+|++|.+||+.|||.|.|.+... ...++.++|+|+..+...|++++.+++..
T Consensus 335 ~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~ 409 (485)
T KOG2190|consen 335 TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSA 409 (485)
T ss_pred cceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccccc
Confidence 23478999999999999999999999999999999999997665 77999999999999999999999887754
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.97 E-value=3.3e-31 Score=281.66 Aligned_cols=247 Identities=24% Similarity=0.408 Sum_probs=193.8
Q ss_pred CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT 263 (541)
Q Consensus 184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~ 263 (541)
..++.+..||.++||.||||+|+.|..|+.++||+|++........+|.|.++|.++. +..|. .++..+++..
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~------v~~aK-~li~evv~r~ 124 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPEN------VEVAK-QLIGEVVSRG 124 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCccc------HHHHH-Hhhhhhhhcc
Confidence 4567789999999999999999999999999999999887667789999999999875 34443 3444455444
Q ss_pred ccc-CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHH
Q 009173 264 SEK-GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV 342 (541)
Q Consensus 264 ~~~-g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~ 342 (541)
... ++.. ......++.+++||++.+|+||||+|++||.|++.+||++.+..|..- +...++.+.|+|++++|+.|.
T Consensus 125 ~~~~~~~~-~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~--~~~~~KplritGdp~~ve~a~ 201 (600)
T KOG1676|consen 125 RPPGGFPD-NQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSI--ATGADKPLRITGDPDKVEQAK 201 (600)
T ss_pred CCCCCccc-cCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCc--CCCCCCceeecCCHHHHHHHH
Confidence 311 1111 112456789999999999999999999999999999999999865421 124678999999999999999
Q ss_pred HHHHHHhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCc
Q 009173 343 YNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPK 422 (541)
Q Consensus 343 ~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~ 422 (541)
.||.++|+|.. .+++ +.. ++
T Consensus 202 ~lV~dil~e~~-~~~~----------------------------------------g~~---~~---------------- 221 (600)
T KOG1676|consen 202 QLVADILREED-DEVP----------------------------------------GSG---GH---------------- 221 (600)
T ss_pred HHHHHHHHhcc-cCCC----------------------------------------ccc---cc----------------
Confidence 99999998521 1000 000 00
Q ss_pred cccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEE
Q 009173 423 LWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKV 502 (541)
Q Consensus 423 ~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I 502 (541)
++.+ .| ...+.+|.||..+||.||||+|++||.|+.+|||+|
T Consensus 222 ---------~g~~----------~g-------------------~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KI 263 (600)
T KOG1676|consen 222 ---------AGVR----------GG-------------------GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKI 263 (600)
T ss_pred ---------cCcC----------cc-------------------ccceeEEeccccceeeEEecCchHHHHHhhccCcee
Confidence 0000 00 124789999999999999999999999999999999
Q ss_pred EEeC-CCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173 503 IVHE-PRLGSTDRIVVISGTPDETQAAQSLLQAFILT 538 (541)
Q Consensus 503 ~I~~-p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~ 538 (541)
+|-. ..+.+.+|.+.|.|++++|++|.+||.++|++
T Consensus 264 QfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 264 QFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE 300 (600)
T ss_pred EeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence 9974 33477899999999999999999999999976
No 5
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=1.1e-31 Score=273.00 Aligned_cols=287 Identities=23% Similarity=0.361 Sum_probs=203.3
Q ss_pred cccCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC-CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHH
Q 009173 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSR 258 (541)
Q Consensus 180 ~~~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~-~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~ 258 (541)
+...-+..+|+|||..+||+||||.|++||.|-..|.|+|+|... ..+..|++++|.|+++. +-+|+.+|++-
T Consensus 193 ~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg------~s~Ac~~ILei 266 (584)
T KOG2193|consen 193 KQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG------TSKACKMILEI 266 (584)
T ss_pred cccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc------hHHHHHHHHHH
Confidence 344567899999999999999999999999999999999999865 56889999999999776 55566555543
Q ss_pred HhhcccccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCc-ccccCCCCCceEEEEcCHHH
Q 009173 259 LIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQ-LLKCISENDRVVQISGEFSK 337 (541)
Q Consensus 259 i~e~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~-~P~~~~s~ervVtItGt~e~ 337 (541)
+..+.... .....+.++++-.+.+||++|||.|.+||+|+++||++|.|.+-. +- .-+.||.+++.|+.++
T Consensus 267 mqkEA~~~------k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels--~ynpERTItVkGsiEa 338 (584)
T KOG2193|consen 267 MQKEAVDD------KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELS--LYNPERTITVKGSIEA 338 (584)
T ss_pred HHHhhhcc------chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhc--ccCccceEEecccHHH
Confidence 32211110 122456789999999999999999999999999999999998321 21 1256999999999999
Q ss_pred HHHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccc-cccccCCCCCCCCCccCCCccCCCCCCC
Q 009173 338 VKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVH-SSVAVSHDFSQPPLTQGMDHLGLSHSLD 416 (541)
Q Consensus 338 V~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~-~~~g~~~~~~r~~~~~~~~~~~~~~~~~ 416 (541)
|.+|..+|+.+|+++...+.....-.- |..+...+..++.. ++.++++ ..
T Consensus 339 c~~AE~eImkKlre~yEnDl~a~s~q~----------~l~P~l~~~~l~~f~ssS~~~~-------------------Ph 389 (584)
T KOG2193|consen 339 CVQAEAEIMKKLRECYENDLAAMSLQC----------HLPPGLNLPALGLFPSSSAVSP-------------------PH 389 (584)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHhhccC----------CCCcccCccccCCCCcccccCC-------------------CC
Confidence 999999999999987544422111100 00000000000000 0000000 00
Q ss_pred CCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHh
Q 009173 417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQ 496 (541)
Q Consensus 417 ~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq 496 (541)
+|++|...++ +. + +.. .-++...+.+.||...+|+|||++|.+||+|.+
T Consensus 390 ~~Ps~v~~a~-------p~-------------~-------~~h----q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~R 438 (584)
T KOG2193|consen 390 FPPSPVTFAS-------PY-------------P-------LFH----QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSR 438 (584)
T ss_pred CCCCccccCC-------Cc-------------h-------hhh----cCcchhheeeeccHHHHHHHHhhcchhHHHHHH
Confidence 0111111000 00 0 000 001346789999999999999999999999999
Q ss_pred HhCCEEEEeCC-CCCCCccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173 497 ISGAKVIVHEP-RLGSTDRIVVISGTPDETQAAQSLLQAFILTGP 540 (541)
Q Consensus 497 ~SGA~I~I~~p-~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~~ 540 (541)
.+||+|+|..| -++.++|+|+|+|.|++..+||..|..+|.+..
T Consensus 439 fagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 439 FAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred hccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence 99999999854 467899999999999999999999999998754
No 6
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=1.9e-26 Score=229.35 Aligned_cols=267 Identities=25% Similarity=0.370 Sum_probs=193.1
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC---CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (541)
Q Consensus 185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~---~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e 261 (541)
.+.+|+|||+..+|.||||||++|.+||++|||+|++++. .|+..||+|.|+|+-+. +......|.++|.|
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea------i~av~efI~dKire 111 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA------LNAVHEFIADKIRE 111 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH------HHHHHHHHHHHHHH
Confidence 3999999999999999999999999999999999999975 78999999999998652 33334445666665
Q ss_pred ccccc-C-CCC--CCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHH
Q 009173 262 GTSEK-G-LDF--SSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337 (541)
Q Consensus 262 ~~~~~-g-~~~--~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~ 337 (541)
..... + .+- ....+..-.++++||++.+|.||||+|.+||.|++++||.|+|+. +.|...+-.||+|++.|++++
T Consensus 112 ~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP-qkpt~~sLqervvt~sge~e~ 190 (402)
T KOG2191|consen 112 KPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP-QKPTGISLQERVVTVSGEPEQ 190 (402)
T ss_pred hHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc-cCCCCccceeEEEEecCCHHH
Confidence 43221 1 110 111222245899999999999999999999999999999999983 334445678999999999999
Q ss_pred HHHHHHHHHHHhhccccCC-CcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCC
Q 009173 338 VKDAVYNVTGRLRDNHFSG-TLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLD 416 (541)
Q Consensus 338 V~~A~~lI~~~l~e~~~~~-~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~ 416 (541)
..+|+.+|.++|.+++... +++ .+|.....|
T Consensus 191 ~~~A~~~IL~Ki~eDpqs~scln--------------~sya~vsGp---------------------------------- 222 (402)
T KOG2191|consen 191 NMKAVSLILQKIQEDPQSGSCLN--------------ISYANVSGP---------------------------------- 222 (402)
T ss_pred HHHHHHHHHHHhhcCCcccceec--------------cchhcccCc----------------------------------
Confidence 9999999999998876332 222 111100000
Q ss_pred CCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHh
Q 009173 417 CPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQ 496 (541)
Q Consensus 417 ~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq 496 (541)
..+++|.+-+-. .....+....+..+.++....|..-|.+|.++-.|..
T Consensus 223 ------------vaNsnPtGspya-------------------~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~ 271 (402)
T KOG2191|consen 223 ------------VANSNPTGSPYA-------------------YQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSG 271 (402)
T ss_pred ------------ccccCCCCCCCC-------------------CCCccccccchhhccccccccccccccccccceeeec
Confidence 000111100000 0000111234567788999999999999999999999
Q ss_pred HhCCEEEEeCC---CCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173 497 ISGAKVIVHEP---RLGSTDRIVVISGTPDETQAAQSLLQAFILT 538 (541)
Q Consensus 497 ~SGA~I~I~~p---~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~ 538 (541)
.+|+.+.|.+. ..+...+ .-+.|.+-.+..|-.+|..++.+
T Consensus 272 ~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~ 315 (402)
T KOG2191|consen 272 FTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVAS 315 (402)
T ss_pred ccccceeeccccccccccccc-ccccchhhhhhhhhhHHHHhhcc
Confidence 99999988743 2344555 77889999999999998887654
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.92 E-value=4.4e-25 Score=225.10 Aligned_cols=240 Identities=26% Similarity=0.396 Sum_probs=189.9
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC---CCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHH
Q 009173 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRL 259 (541)
Q Consensus 183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~---~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i 259 (541)
..++.+|++-.+..||++|||.|.+||+|+.+||++|.|++- .....||.|++.|+-+. +..|-.+|+.++
T Consensus 277 ~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEa------c~~AE~eImkKl 350 (584)
T KOG2193|consen 277 AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEA------CVQAEAEIMKKL 350 (584)
T ss_pred hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHH------HHHHHHHHHHHH
Confidence 467899999999999999999999999999999999999863 33467999999996553 677777777766
Q ss_pred hhc---cc---------ccCC--------CCC---------C-------------CCCceeEEEEEeccccccccccccc
Q 009173 260 IEG---TS---------EKGL--------DFS---------S-------------NKGLLVNARLVVASNQVGCLLGKGG 297 (541)
Q Consensus 260 ~e~---~~---------~~g~--------~~~---------~-------------~~~~~vt~~l~VP~~~vG~IIGKgG 297 (541)
.+. +. ..++ .+. + .......++|.||...||.||||+|
T Consensus 351 re~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG 430 (584)
T KOG2193|consen 351 RECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKG 430 (584)
T ss_pred HHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcc
Confidence 542 11 0000 000 0 0113446899999999999999999
Q ss_pred chhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCCcccccccCCCCccccCCCCC
Q 009173 298 TIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYS 377 (541)
Q Consensus 298 ~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~ 377 (541)
..||.|.+.+||.|+|..-..|+ ..+|.|+|+|.+++.-+|+-.|..+|.|..|..
T Consensus 431 ~hIKql~RfagASiKIappE~pd---vseRMViItGppeaqfKAQgrifgKikEenf~~--------------------- 486 (584)
T KOG2193|consen 431 QHIKQLSRFAGASIKIAPPEIPD---VSERMVIITGPPEAQFKAQGRIFGKIKEENFFL--------------------- 486 (584)
T ss_pred hhHHHHHHhccceeeecCCCCCC---cceeEEEecCChHHHHhhhhhhhhhhhhhccCC---------------------
Confidence 99999999999999998544665 789999999999999999999999997643210
Q ss_pred CCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCccc
Q 009173 378 RLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLEL 457 (541)
Q Consensus 378 ~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~ 457 (541)
|. ..
T Consensus 487 -------------------------------------------Pk------------------------------ee--- 490 (584)
T KOG2193|consen 487 -------------------------------------------PK------------------------------EE--- 490 (584)
T ss_pred -------------------------------------------ch------------------------------hh---
Confidence 00 00
Q ss_pred CCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC-CCCCC-ccEEEEEeCHHHHHHHHHHHHHH
Q 009173 458 GSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP-RLGST-DRIVVISGTPDETQAAQSLLQAF 535 (541)
Q Consensus 458 ~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p-~~~s~-~RiItIsGtpeqV~~Aq~LI~~~ 535 (541)
.....+|.||...+|+||||||.|+++|+..|+|.|.|+++ .+|.+ .-+|.|.|.--+++.||.-|.+.
T Consensus 491 ---------vklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~i 561 (584)
T KOG2193|consen 491 ---------VKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHI 561 (584)
T ss_pred ---------heeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHH
Confidence 12467999999999999999999999999999999999843 34443 45677999999999999998887
Q ss_pred Hh
Q 009173 536 IL 537 (541)
Q Consensus 536 I~ 537 (541)
+.
T Consensus 562 v~ 563 (584)
T KOG2193|consen 562 VN 563 (584)
T ss_pred HH
Confidence 75
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.87 E-value=1.6e-21 Score=194.46 Aligned_cols=164 Identities=24% Similarity=0.447 Sum_probs=135.0
Q ss_pred eeEEEEEecccccccccccccchhhhhhcccCeeEEEc--cCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcccc
Q 009173 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF 354 (541)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~--~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~ 354 (541)
.+.++++||+..+|.||||||++|.++|++|||+|+++ +|++|. ++||++.|+|+.+++....+.|.++|+|.+.
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG---TTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG---TTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC---ccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 47899999999999999999999999999999999999 678997 8999999999999999999999999997541
Q ss_pred CCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccC
Q 009173 355 SGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHL 434 (541)
Q Consensus 355 ~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~ 434 (541)
... - ++.. . .|+ . + .
T Consensus 115 ~~~----------------k-------~v~~------------------------------~---~pq-----t-~---~ 129 (402)
T KOG2191|consen 115 AVA----------------K-------PVDI------------------------------L---QPQ-----T-P---D 129 (402)
T ss_pred hhc----------------C-------Cccc------------------------------c---CCC-----C-c---c
Confidence 100 0 0000 0 000 0 0 0
Q ss_pred CCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCC---CC
Q 009173 435 RGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL---GS 511 (541)
Q Consensus 435 ~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~---~s 511 (541)
| ....++.||...+|.||||+|.+||.|++++||.|+|...++ .-
T Consensus 130 r--------------------------------~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sL 177 (402)
T KOG2191|consen 130 R--------------------------------IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISL 177 (402)
T ss_pred c--------------------------------cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccc
Confidence 0 023789999999999999999999999999999999984332 22
Q ss_pred CccEEEEEeCHHHHHHHHHHHHHHHhcCC
Q 009173 512 TDRIVVISGTPDETQAAQSLLQAFILTGP 540 (541)
Q Consensus 512 ~~RiItIsGtpeqV~~Aq~LI~~~I~~~~ 540 (541)
.+|.||++|++++..+|.+||.++|.++.
T Consensus 178 qervvt~sge~e~~~~A~~~IL~Ki~eDp 206 (402)
T KOG2191|consen 178 QERVVTVSGEPEQNMKAVSLILQKIQEDP 206 (402)
T ss_pred eeEEEEecCCHHHHHHHHHHHHHHhhcCC
Confidence 68999999999999999999999998753
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.70 E-value=1.9e-16 Score=171.24 Aligned_cols=158 Identities=30% Similarity=0.479 Sum_probs=129.8
Q ss_pred eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc---------CHHHHHHHHHHHHH
Q 009173 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG---------EFSKVKDAVYNVTG 347 (541)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG---------t~e~V~~A~~lI~~ 347 (541)
..+++|+++...+|.||||+|.+||+|+..+.++|+|. +..|+ ..+|+|+|+| ..+++.+|..+|..
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~-~~~~~---c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~ 117 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVN-ESLPG---CPERIITITGNRVELNLSPATDALFKAFDMIVF 117 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceee-cCCCC---CCcceEEEecccccccCCchHHHHHHHHHHHhh
Confidence 34589999999999999999999999999999999997 23555 4699999999 99999999999988
Q ss_pred HhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccc
Q 009173 348 RLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQ 427 (541)
Q Consensus 348 ~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~ 427 (541)
.+.++....
T Consensus 118 ~~~~d~~~~----------------------------------------------------------------------- 126 (485)
T KOG2190|consen 118 KLEEDDEAA----------------------------------------------------------------------- 126 (485)
T ss_pred ccccccccc-----------------------------------------------------------------------
Confidence 775221000
Q ss_pred ccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCC
Q 009173 428 TVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEP 507 (541)
Q Consensus 428 ~~~g~~~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p 507 (541)
.++. + ...+ ...++++.||.+.+|+||||+|+.||+||+.|||+|.|...
T Consensus 127 ----------~d~~------------~--~~~~------~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~ 176 (485)
T KOG2190|consen 127 ----------EDNG------------E--DASG------PEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD 176 (485)
T ss_pred ----------ccCC------------c--cccC------CceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC
Confidence 0000 0 0000 02689999999999999999999999999999999999854
Q ss_pred -CCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173 508 -RLGSTDRIVVISGTPDETQAAQSLLQAFILTG 539 (541)
Q Consensus 508 -~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~ 539 (541)
.+.+++|.|+|+|.+++|.+|...|..+|...
T Consensus 177 ~lP~ster~V~IsG~~~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 177 MLPNSTERAVTISGEPDAVKKALVQISSRLLEN 209 (485)
T ss_pred CCCcccceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence 68889999999999999999999999999863
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.65 E-value=9.7e-16 Score=149.32 Aligned_cols=217 Identities=19% Similarity=0.364 Sum_probs=151.1
Q ss_pred hhhhccCceeeeccccccCCCCCccCCCCCcccccCCCCcccccccccCCCcccccccchhh-cccCCceEEEEEecccc
Q 009173 118 LSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDA-RTQQQEVSFRILCSNDK 196 (541)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~rilvP~~~ 196 (541)
+-+--||+.+.++|-+--.-..+ .-..+-+++++++-....++. +. ..-.+.++. .+-...+.+||||..+.
T Consensus 61 avigkgg~nik~lr~d~na~v~v-pds~~peri~tisad~~ti~~----il--k~iip~lee~f~~~~pce~rllihqs~ 133 (390)
T KOG2192|consen 61 AVIGKGGKNIKALRTDYNASVSV-PDSSGPERILTISADIETIGE----IL--KKIIPTLEEGFQLPSPCELRLLIHQSL 133 (390)
T ss_pred ceeccccccHHHHhhhccceeec-cCCCCCceeEEEeccHHHHHH----HH--HHHhhhhhhCCCCCCchhhhhhhhhhh
Confidence 56778899999888663110000 012234566666533211110 00 011122221 22344578999999999
Q ss_pred ccceeccCchHHHHHHHHhCCeEEecC-CCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc----------
Q 009173 197 VGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE---------- 265 (541)
Q Consensus 197 vG~IIGKgG~~Ik~Iq~eTGa~I~I~~-~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~---------- 265 (541)
+|.|||++|+.||.|+++..|+++|-- .-|.+.+|+|.|.|.++. ++..+..|++.+.|..+.
T Consensus 134 ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~------v~~~i~~il~~i~e~pikgsa~py~p~f 207 (390)
T KOG2192|consen 134 AGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKR------VVECIKIILDLISESPIKGSAQPYDPNF 207 (390)
T ss_pred ccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcch------HHHHHHHHHHHhhcCCcCCcCCcCCccc
Confidence 999999999999999999999999763 478899999999998775 666666666655441100
Q ss_pred ---------------------------------------------cC---------CCC---------------------
Q 009173 266 ---------------------------------------------KG---------LDF--------------------- 270 (541)
Q Consensus 266 ---------------------------------------------~g---------~~~--------------------- 270 (541)
.+ .+|
T Consensus 208 yd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~Sewqma 287 (390)
T KOG2192|consen 208 YDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMA 287 (390)
T ss_pred cCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccc
Confidence 00 000
Q ss_pred --------------------CCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEE
Q 009173 271 --------------------SSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQ 330 (541)
Q Consensus 271 --------------------~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVt 330 (541)
+.-.+...|.++.||.+.-|.||||||+.|++|+.++||.|+|.. .+ .++.||+++
T Consensus 288 YePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide-pl---eGsedrIit 363 (390)
T KOG2192|consen 288 YEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE-PL---EGSEDRIIT 363 (390)
T ss_pred cCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC-cC---CCCCceEEE
Confidence 000124467899999999999999999999999999999999951 12 347899999
Q ss_pred EEcCHHHHHHHHHHHHHHhhc
Q 009173 331 ISGEFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 331 ItGt~e~V~~A~~lI~~~l~e 351 (541)
|+|+.++++.|++++...++.
T Consensus 364 ItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 364 ITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred EeccHHHHhhHHHHHHHHHHh
Confidence 999999999999999998874
No 11
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.63 E-value=1.2e-15 Score=144.81 Aligned_cols=136 Identities=24% Similarity=0.355 Sum_probs=104.3
Q ss_pred EEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEE---EcCHHHHHHHHHHHHHHhhccccCCCc
Q 009173 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI---SGEFSKVKDAVYNVTGRLRDNHFSGTL 358 (541)
Q Consensus 282 l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtI---tGt~e~V~~A~~lI~~~l~e~~~~~~~ 358 (541)
+.||.+.+|.|||+||++|+.|+++|||+|.|..+ +..|.| +++++++.+|..+|..+.+.....+.+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~ 72 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE---------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKAL 72 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC---------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 57899999999999999999999999999999522 357888 899999999999999977521100000
Q ss_pred ccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCC
Q 009173 359 NTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSS 438 (541)
Q Consensus 359 ~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~ 438 (541)
.- + + .. +
T Consensus 73 ~l------------------------~-------------------g-------d~---------y-------------- 79 (172)
T TIGR03665 73 KL------------------------L-------------------D-------DD---------Y-------------- 79 (172)
T ss_pred Hh------------------------c-------------------C-------Cc---------c--------------
Confidence 00 0 0 00 0
Q ss_pred CCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEec---------cCcccceeeCCcchHHHHHhHhCCEEEEeCCCC
Q 009173 439 DVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVP---------ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL 509 (541)
Q Consensus 439 d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP---------~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~ 509 (541)
.-.-+.|+ ...+|+|||++|++++.|+..|||+|.|++
T Consensus 80 ------------------------------~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~--- 126 (172)
T TIGR03665 80 ------------------------------MLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG--- 126 (172)
T ss_pred ------------------------------eEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC---
Confidence 00001111 237899999999999999999999999963
Q ss_pred CCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173 510 GSTDRIVVISGTPDETQAAQSLLQAFI 536 (541)
Q Consensus 510 ~s~~RiItIsGtpeqV~~Aq~LI~~~I 536 (541)
..|.|.|++++++.|+.+|+.+|
T Consensus 127 ----~~v~i~G~~~~~~~A~~~i~~li 149 (172)
T TIGR03665 127 ----KTVGIIGDPEQVQIAREAIEMLI 149 (172)
T ss_pred ----CEEEEECCHHHHHHHHHHHHHHH
Confidence 67999999999999999999988
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.57 E-value=2.3e-14 Score=137.07 Aligned_cols=149 Identities=22% Similarity=0.323 Sum_probs=106.9
Q ss_pred eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE----cCHHHHHHHHHHHHHHhhccc
Q 009173 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS----GEFSKVKDAVYNVTGRLRDNH 353 (541)
Q Consensus 278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt----Gt~e~V~~A~~lI~~~l~e~~ 353 (541)
....+.||.+.+|.|||++|++|+.|+++|||+|.+..+ +..|.|. ++++++.+|+.+|..+++...
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS 73 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC
Confidence 356899999999999999999999999999999999522 3678885 899999999999999886211
Q ss_pred cCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccccccccc
Q 009173 354 FSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVH 433 (541)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~ 433 (541)
..+.+.. + + .. +...
T Consensus 74 ~e~A~~l------------------------~-------------------g-------d~---------y~~~------ 88 (180)
T PRK13763 74 PEKALRL------------------------L-------------------D-------DD---------YVLE------ 88 (180)
T ss_pred HHHHHHH------------------------h-------------------C-------CC---------ceEE------
Confidence 0000000 0 0 00 0000
Q ss_pred CCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCc
Q 009173 434 LRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTD 513 (541)
Q Consensus 434 ~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~ 513 (541)
--...++. .. . ......+|+|||++|++++.|+..|||+|.|.+
T Consensus 89 Vi~i~~~~------------------~~----------~-~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------- 132 (180)
T PRK13763 89 VIDLSDYG------------------DS----------P-NALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------- 132 (180)
T ss_pred EEEhhhcc------------------CC----------h-hHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------
Confidence 00000000 00 0 011237899999999999999999999999963
Q ss_pred cEEEEEeCHHHHHHHHHHHHHHH
Q 009173 514 RIVVISGTPDETQAAQSLLQAFI 536 (541)
Q Consensus 514 RiItIsGtpeqV~~Aq~LI~~~I 536 (541)
+.|.|.|++++++.|+..|+..+
T Consensus 133 ~~v~i~G~~~~~~~A~~~I~~li 155 (180)
T PRK13763 133 KTVAIIGDPEQVEIAREAIEMLI 155 (180)
T ss_pred CEEEEEeCHHHHHHHHHHHHHHH
Confidence 45999999999999999999988
No 13
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.57 E-value=9.7e-15 Score=138.70 Aligned_cols=138 Identities=20% Similarity=0.269 Sum_probs=98.8
Q ss_pred EEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEe---cCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT---ASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (541)
Q Consensus 190 ilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~It---G~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~ 266 (541)
|.||.+.+|.|||+||++||.|+++|||+|++.+ ++..|.|. +.+. .+++|...|.........+.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~------~i~kA~~~I~~i~~gf~~e~ 70 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL------AVMKAREVVKAIGRGFSPEK 70 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH------HHHHHHHHHHHHHcCCCHHH
Confidence 5689999999999999999999999999999984 33568883 3222 36666665544221101100
Q ss_pred CCCCCCCCCceeEEE-EEecc---------cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHH
Q 009173 267 GLDFSSNKGLLVNAR-LVVAS---------NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336 (541)
Q Consensus 267 g~~~~~~~~~~vt~~-l~VP~---------~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e 336 (541)
-+ .. .+..++.+ +.|+. ..+|+|||++|++++.|++.|||+|.|. +..|.|.|+++
T Consensus 71 A~--~l-~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G~~~ 136 (172)
T TIGR03665 71 AL--KL-LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIGDPE 136 (172)
T ss_pred HH--Hh-cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEECCHH
Confidence 00 00 01112222 23333 3689999999999999999999999994 36799999999
Q ss_pred HHHHHHHHHHHHhhcc
Q 009173 337 KVKDAVYNVTGRLRDN 352 (541)
Q Consensus 337 ~V~~A~~lI~~~l~e~ 352 (541)
+++.|..+|.+++.+.
T Consensus 137 ~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 137 QVQIAREAIEMLIEGA 152 (172)
T ss_pred HHHHHHHHHHHHHcCC
Confidence 9999999999999643
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.50 E-value=9.5e-14 Score=132.82 Aligned_cols=141 Identities=18% Similarity=0.225 Sum_probs=100.0
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEe----cCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT----ASEGPESRYSPAQKAVVLVFSRLIE 261 (541)
Q Consensus 186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~It----G~~~~~~~~s~a~~Ai~~i~~~i~e 261 (541)
+...+.||.+.+|.|||++|++||.|+++|||+|++.+ ++..|.|. ++++ .+++|...|.+....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~------~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPL------AVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHH------HHHHHHHHHHHHhcC
Confidence 46778999999999999999999999999999999984 34677886 3222 256666555442221
Q ss_pred cccccCCCCCCCCCceeEEEE-Eec---------ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEE
Q 009173 262 GTSEKGLDFSSNKGLLVNARL-VVA---------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI 331 (541)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~l-~VP---------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtI 331 (541)
...+..+. . .+..+..++ .|. ...+|+|||++|++++.|++.|||+|.|. ++.|.|
T Consensus 72 f~~e~A~~--l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~-----------~~~v~i 137 (180)
T PRK13763 72 FSPEKALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY-----------GKTVAI 137 (180)
T ss_pred CCHHHHHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc-----------CCEEEE
Confidence 01110000 0 011112221 111 13689999999999999999999999994 235899
Q ss_pred EcCHHHHHHHHHHHHHHhhc
Q 009173 332 SGEFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 332 tGt~e~V~~A~~lI~~~l~e 351 (541)
.|++++++.|...|..+++.
T Consensus 138 ~G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 138 IGDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred EeCHHHHHHHHHHHHHHHcC
Confidence 99999999999999999964
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.43 E-value=2.9e-13 Score=108.07 Aligned_cols=63 Identities=40% Similarity=0.675 Sum_probs=58.6
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCC-CCCccEEEEEeCHHHHHHHHHHHH
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRL-GSTDRIVVISGTPDETQAAQSLLQ 533 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~-~s~~RiItIsGtpeqV~~Aq~LI~ 533 (541)
.+|.||.+++|+|||++|++|++|++.|||+|.|.+... +..+|.|+|+|++++++.|..||+
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 589999999999999999999999999999999996554 678999999999999999999984
No 16
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.36 E-value=4e-12 Score=135.08 Aligned_cols=292 Identities=19% Similarity=0.258 Sum_probs=181.3
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhh
Q 009173 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (541)
Q Consensus 182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e 261 (541)
.+.++.+++.|+...|-.+|||+|++|+.|+..++++|.+..... .+++.-++.|.+.+ ++++..+ ++.++.+
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~-g~e~~~~~~~~p~~---v~~a~a~---~~~~~~~ 136 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV-GDERVLLISGFPVQ---VCKAKAA---IHQILTE 136 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC-CcccchhhccCCCC---CChHHHH---HHHHHhc
Confidence 456789999999999999999999999999999999999986432 35677777775443 3344433 3444432
Q ss_pred cccccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHH
Q 009173 262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341 (541)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A 341 (541)
+..+...+.+|...+++|+|++|.++++|+..++|+|.+..+.. ..-.+...|.|....+..|
T Consensus 137 -------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr----~g~~~~~~i~~qqk~~~~a 199 (608)
T KOG2279|consen 137 -------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR----LGLSRLIKISGQQKEVAAA 199 (608)
T ss_pred -------------CCcccccccchhhhcccccccchhhhcchhcccccccccccccc----cccccceecccccchHHHH
Confidence 34566788999999999999999999999999999999863321 1346788888999999999
Q ss_pred HHHHHHHhhccccCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCC
Q 009173 342 VYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSP 421 (541)
Q Consensus 342 ~~lI~~~l~e~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p 421 (541)
..++.+++.++.-.-. .++...-- -.+...|.+... -++.. ++....+.-..+...
T Consensus 200 ~~~~~~~~~edeelv~-~~~e~~q~--rvprk~p~n~~~----~~m~~--------------~~~s~~~h~~~~t~~--- 255 (608)
T KOG2279|consen 200 KHLILEKVSEDEELVK-RIAESAQT--RVPRKQPINVRR----EDMTE--------------PGGAGEPHLWKNTSS--- 255 (608)
T ss_pred HhhhhccccchhHHhh-hchhhccc--CCCCCCCccccc----hhhcc--------------cccCCccccCccchh---
Confidence 9999999976542110 00100000 000011111100 00000 000000000000000
Q ss_pred ccccccccccccCCCCCCCC------CCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHH
Q 009173 422 KLWTAQTVTGVHLRGSSDVG------RGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLR 495 (541)
Q Consensus 422 ~~~~~~~~~g~~~~g~~d~~------~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Ir 495 (541)
.+.++.++.+ +..++.. +.|... . .|....-......+|.+|...+|.+||+.|.+++.+.
T Consensus 256 --s~spg~~~~~-~eg~dm~v~vsk~~s~~~~----~------d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~ys 322 (608)
T KOG2279|consen 256 --SMSPGAPLVT-KEGGDMAVVVSKEGSWEKP----S------DDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYS 322 (608)
T ss_pred --ccCCCCCCcc-cCCCcceeEEecccccCCc----c------ccccccccccccceeecCcccccchhhhhhhhhhhhh
Confidence 0001111111 0001100 011111 0 1111122234678999999999999999999999999
Q ss_pred hHhCCEEEEeC-CCCCC--CccEEEEEeCHHHHHHHHHHHHH
Q 009173 496 QISGAKVIVHE-PRLGS--TDRIVVISGTPDETQAAQSLLQA 534 (541)
Q Consensus 496 q~SGA~I~I~~-p~~~s--~~RiItIsGtpeqV~~Aq~LI~~ 534 (541)
..|++.+.|-- +..+. .-.++.+.|+..-++.+-.||..
T Consensus 323 sasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 323 SASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTV 364 (608)
T ss_pred hccCccceEEeccccchhhhhhhheecchhHHHHHHHhhhhc
Confidence 99999988863 22221 22678899999999999999873
No 17
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.29 E-value=4.6e-12 Score=101.12 Aligned_cols=65 Identities=42% Similarity=0.647 Sum_probs=58.0
Q ss_pred EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHH
Q 009173 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT 346 (541)
Q Consensus 279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~ 346 (541)
+++|+||.+++|+||||+|.+|++|+++|||+|.+..+..+ ..++|+|+|+|+++++++|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP---GSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCC---CCCceEEEEEeCHHHHHHHHHhhC
Confidence 36899999999999999999999999999999999854332 367899999999999999999873
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.25 E-value=1e-11 Score=97.95 Aligned_cols=61 Identities=21% Similarity=0.449 Sum_probs=55.9
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHH
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQ 533 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~ 533 (541)
.++.||.+++|+|||++|++|++|++.|||+|.|++.. ..++.|+|+|+++++..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999997543 57899999999999999999874
No 19
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.24 E-value=7.2e-12 Score=98.13 Aligned_cols=60 Identities=30% Similarity=0.629 Sum_probs=55.3
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHH
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLL 532 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI 532 (541)
|.+|.||.+++|+|||++|++|++|++.|||+|.|++. + ....|+|+|+++++++|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999765 3 556999999999999999987
No 20
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.24 E-value=2.3e-11 Score=95.92 Aligned_cols=63 Identities=33% Similarity=0.693 Sum_probs=58.4
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHH
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQ 533 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~ 533 (541)
.+|.||.+++|+|||++|++|++|++.|||+|.|.+...+..++.|+|+|+.++++.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 578999999999999999999999999999999987666678899999999999999999874
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.18 E-value=5.7e-11 Score=93.72 Aligned_cols=58 Identities=19% Similarity=0.437 Sum_probs=53.4
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHH
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQ 533 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~ 533 (541)
+..+.||.+++|+|||+||++|++|++.|||+|.|++ ++.|.|+|+ +++++.|+.+|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence 5688999999999999999999999999999999975 368999999 999999999874
No 22
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.03 E-value=2e-10 Score=89.96 Aligned_cols=60 Identities=35% Similarity=0.528 Sum_probs=53.8
Q ss_pred EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHH
Q 009173 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (541)
Q Consensus 279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI 345 (541)
|.+|.||.+++|+|||++|++|++|+++|||+|.|+.+ ..+..|+|+|++++|++|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999743 1245899999999999999886
No 23
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.03 E-value=3.6e-10 Score=89.03 Aligned_cols=60 Identities=20% Similarity=0.333 Sum_probs=54.3
Q ss_pred EEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHH
Q 009173 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (541)
Q Consensus 280 ~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI 345 (541)
.++.||..++|+|||++|++|++|+++|||+|.++... +.++.|+|+|+.++|..|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997432 4578999999999999999886
No 24
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.02 E-value=5.3e-10 Score=88.20 Aligned_cols=58 Identities=21% Similarity=0.313 Sum_probs=52.5
Q ss_pred eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC-HHHHHHHHHHH
Q 009173 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNV 345 (541)
Q Consensus 278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt-~e~V~~A~~lI 345 (541)
.+..+.||.+++|+||||+|++|++|+++|||+|.|.. ++.|.|+|+ .++++.|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC----------CCEEEEEeCCHHHHHHHHHHh
Confidence 35688999999999999999999999999999999942 467999998 99999999887
No 25
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.90 E-value=2.7e-09 Score=84.02 Aligned_cols=53 Identities=34% Similarity=0.616 Sum_probs=48.3
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCC
Q 009173 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (541)
Q Consensus 188 ~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~ 240 (541)
.+|.||..++|.|||++|++|++|+++|||+|.|.+...+..++.|.|.|..+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~ 54 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPE 54 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHH
Confidence 57999999999999999999999999999999999765567899999999854
No 26
>PF13014 KH_3: KH domain
Probab=98.88 E-value=3e-09 Score=77.81 Aligned_cols=42 Identities=40% Similarity=0.743 Sum_probs=38.9
Q ss_pred cccceeccCchHHHHHHHHhCCeEEecC-CCCCCCcceEEEec
Q 009173 196 KVGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTA 237 (541)
Q Consensus 196 ~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~-~~~~~~eRvV~ItG 237 (541)
++|+||||+|++|++|+++|||+|+|++ ..++..+|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4899999999999999999999999998 46788999999997
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=98.87 E-value=1.3e-08 Score=80.09 Aligned_cols=66 Identities=26% Similarity=0.606 Sum_probs=59.5
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFI 536 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I 536 (541)
.+.+|.||.+++|++||++|++|++|++.+|++|.+..... ....|+|.|++++++.|+.+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 56899999999999999999999999999999999964332 5789999999999999999998876
No 28
>PF13014 KH_3: KH domain
Probab=98.86 E-value=3.9e-09 Score=77.19 Aligned_cols=42 Identities=33% Similarity=0.683 Sum_probs=38.7
Q ss_pred cccceeeCCcchHHHHHhHhCCEEEEeC-CCCCCCccEEEEEe
Q 009173 479 VIGSVYGENGSNLLRLRQISGAKVIVHE-PRLGSTDRIVVISG 520 (541)
Q Consensus 479 ~vG~IIGkgGs~Ik~Irq~SGA~I~I~~-p~~~s~~RiItIsG 520 (541)
++|+|||++|++|++|+++|||+|+|++ ..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999986 55677899999998
No 29
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.65 E-value=1.6e-08 Score=107.99 Aligned_cols=146 Identities=25% Similarity=0.388 Sum_probs=122.7
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcccc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF 354 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~ 354 (541)
...+.++++|+...+-+++||+|.+|+.|+..++++|.+-.++.+ .+++-.+.|-+.++..|...++.++.++.
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~~- 138 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-----DERVLLISGFPVQVCKAKAAIHQILTENT- 138 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-----cccchhhccCCCCCChHHHHHHHHHhcCC-
Confidence 356788999999999999999999999999999999999866554 36677777899999999999999885210
Q ss_pred CCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccC
Q 009173 355 SGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHL 434 (541)
Q Consensus 355 ~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~ 434 (541)
T Consensus 139 -------------------------------------------------------------------------------- 138 (608)
T KOG2279|consen 139 -------------------------------------------------------------------------------- 138 (608)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCcc
Q 009173 435 RGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDR 514 (541)
Q Consensus 435 ~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~R 514 (541)
.+..+..+|...+++|+|++|.++..|+.-|+|+|.+......-..+
T Consensus 139 ---------------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~ 185 (608)
T KOG2279|consen 139 ---------------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSR 185 (608)
T ss_pred ---------------------------------cccccccchhhhcccccccchhhhcchhccccccccccccccccccc
Confidence 02235577889999999999999999999999999998664444678
Q ss_pred EEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173 515 IVVISGTPDETQAAQSLLQAFILTG 539 (541)
Q Consensus 515 iItIsGtpeqV~~Aq~LI~~~I~~~ 539 (541)
.+.|.|....+..|+.++.+.++..
T Consensus 186 ~~~i~~qqk~~~~a~~~~~~~~~ed 210 (608)
T KOG2279|consen 186 LIKISGQQKEVAAAKHLILEKVSED 210 (608)
T ss_pred ceecccccchHHHHHhhhhccccch
Confidence 8999999999999999999988653
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.63 E-value=1.1e-07 Score=74.61 Aligned_cols=66 Identities=32% Similarity=0.553 Sum_probs=58.6
Q ss_pred eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL 349 (541)
Q Consensus 278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l 349 (541)
.+.++.||...+|.+||++|.+|++|++.||++|.+..+. .....+.|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 5778999999999999999999999999999999996321 14678999999999999999998876
No 31
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.62 E-value=2.3e-07 Score=88.48 Aligned_cols=142 Identities=21% Similarity=0.284 Sum_probs=100.7
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc
Q 009173 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE 265 (541)
Q Consensus 186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~ 265 (541)
..+.+.||...+|.+||+.|++.+.|.+.+++++.+. ..+..|.|..+....++ ...++|...+.+ +..
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp-~~~~ka~d~VkA--Igr--- 76 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP-LALLKARDVVKA--IGR--- 76 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh-HHHHHHHHHHHH--Hhc---
Confidence 4567899999999999999999999999999999997 56778999876321111 124455433322 211
Q ss_pred cCCCCCCC---CCceeEEEE------Eec-----ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEE
Q 009173 266 KGLDFSSN---KGLLVNARL------VVA-----SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI 331 (541)
Q Consensus 266 ~g~~~~~~---~~~~vt~~l------~VP-----~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtI 331 (541)
|+++... ....+.+.+ .-+ ....|+|||++|.|.+-|++.|||.|.|. +..|.|
T Consensus 77 -GF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-----------g~tVai 144 (194)
T COG1094 77 -GFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-----------GKTVAI 144 (194)
T ss_pred -CCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-----------CcEEEE
Confidence 2221100 000111111 111 22459999999999999999999999995 357999
Q ss_pred EcCHHHHHHHHHHHHHHhh
Q 009173 332 SGEFSKVKDAVYNVTGRLR 350 (541)
Q Consensus 332 tGt~e~V~~A~~lI~~~l~ 350 (541)
.|.+++|+.|...|..++.
T Consensus 145 iG~~~~v~iAr~AVemli~ 163 (194)
T COG1094 145 IGGFEQVEIAREAVEMLIN 163 (194)
T ss_pred ecChhhhHHHHHHHHHHHc
Confidence 9999999999999999996
No 32
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.55 E-value=4.4e-07 Score=104.02 Aligned_cols=233 Identities=18% Similarity=0.243 Sum_probs=159.8
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCC-CCCHHHHHHHHHHHH---
Q 009173 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES-RYSPAQKAVVLVFSR--- 258 (541)
Q Consensus 183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~-~~s~a~~Ai~~i~~~--- 258 (541)
..-+..++.+-...++.+||+||.+++.++.++.+.|.|+...- ......|.|..+... .....+.++.++-..
T Consensus 198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~ 275 (753)
T KOG2208|consen 198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSINVEIQEALTRLESEFDY 275 (753)
T ss_pred ceeEEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceehhhhhHHHHHHhcChhhh
Confidence 34478899999999999999999999999999999999986411 111111112100000 000011221111110
Q ss_pred ----------------------Hhh---------cc-ccc-------CCCCC-------------CCCCceeEEEEEecc
Q 009173 259 ----------------------LIE---------GT-SEK-------GLDFS-------------SNKGLLVNARLVVAS 286 (541)
Q Consensus 259 ----------------------i~e---------~~-~~~-------g~~~~-------------~~~~~~vt~~l~VP~ 286 (541)
+.. .. ..+ +.+.+ .-....+.+.+.|-.
T Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~ 355 (753)
T KOG2208|consen 276 DEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP 355 (753)
T ss_pred hhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence 000 00 000 00000 001244778899999
Q ss_pred cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhccccCCCcccccccCC
Q 009173 287 NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRST 366 (541)
Q Consensus 287 ~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~~~~~~~~~~~~~ 366 (541)
..+..++||+|.+|.+|++.+.+.+.+... ++++..+.++|...++.+|...+...+.+-..
T Consensus 356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------------ 417 (753)
T KOG2208|consen 356 EELKFVIGKKGANIEKIREESQVKIDLPKQ------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN------------ 417 (753)
T ss_pred HhhhhhcCCCCccHHHHHHhhhhceecccc------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc------------
Confidence 999999999999999999999999999631 35678899999999999999999988854210
Q ss_pred CCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcC
Q 009173 367 SSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQ 446 (541)
Q Consensus 367 ~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~~g~~d~~~~~~~ 446 (541)
+
T Consensus 418 ------------------------------------------------------~------------------------- 418 (753)
T KOG2208|consen 418 ------------------------------------------------------S------------------------- 418 (753)
T ss_pred ------------------------------------------------------c-------------------------
Confidence 0
Q ss_pred CCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHH
Q 009173 447 GLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQ 526 (541)
Q Consensus 447 g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~ 526 (541)
....++.+|+..+.++||.+|..|+.|...+|+ +.|..+........+++.|.-..+.
T Consensus 419 ---------------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~ 476 (753)
T KOG2208|consen 419 ---------------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVE 476 (753)
T ss_pred ---------------------cccceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCCCcccccceEeccccccc
Confidence 023478999999999999999999999999997 7776666666777888888877777
Q ss_pred HHHHHHHHHH
Q 009173 527 AAQSLLQAFI 536 (541)
Q Consensus 527 ~Aq~LI~~~I 536 (541)
.++.++..+.
T Consensus 477 ~~~~~~~~~~ 486 (753)
T KOG2208|consen 477 KSVSLLKALK 486 (753)
T ss_pred hhHHHHHhhh
Confidence 7666555443
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.54 E-value=4.4e-07 Score=86.58 Aligned_cols=146 Identities=18% Similarity=0.257 Sum_probs=103.9
Q ss_pred EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-----CHHHHHHHHHHHHHHhhccc
Q 009173 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-----EFSKVKDAVYNVTGRLRDNH 353 (541)
Q Consensus 279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-----t~e~V~~A~~lI~~~l~e~~ 353 (541)
...+.||...+|.+||+.|.+-+.|.+.+++++.+. +.+..|+|.- +|..+.+|...|..+-+-..
T Consensus 9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD---------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~ 79 (194)
T COG1094 9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID---------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFP 79 (194)
T ss_pred eeeeecCchhheeeecccccchHHHHhhcCeEEEEE---------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCC
Confidence 456899999999999999999999999999999995 3345666654 57889999888887664211
Q ss_pred cCCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCcccccccccccc
Q 009173 354 FSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVH 433 (541)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~ 433 (541)
....+.
T Consensus 80 pe~A~~-------------------------------------------------------------------------- 85 (194)
T COG1094 80 PEKALK-------------------------------------------------------------------------- 85 (194)
T ss_pred HHHHHH--------------------------------------------------------------------------
Confidence 000000
Q ss_pred CCCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEe-c----cCcccceeeCCcchHHHHHhHhCCEEEEeCCC
Q 009173 434 LRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIV-P----ENVIGSVYGENGSNLLRLRQISGAKVIVHEPR 508 (541)
Q Consensus 434 ~~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~I-P----~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~ 508 (541)
+... ...+..-...++.- + ....|+|||++|.+.+.|...|||.|.|..
T Consensus 86 -----------------------LL~d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-- 139 (194)
T COG1094 86 -----------------------LLED-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG-- 139 (194)
T ss_pred -----------------------HhcC-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC--
Confidence 0000 00000000000011 1 235699999999999999999999999964
Q ss_pred CCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173 509 LGSTDRIVVISGTPDETQAAQSLLQAFILT 538 (541)
Q Consensus 509 ~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~ 538 (541)
..|-|.|.+++++.|+..|..+|..
T Consensus 140 -----~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 140 -----KTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred -----cEEEEecChhhhHHHHHHHHHHHcC
Confidence 5799999999999999999998864
No 34
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.16 E-value=4.8e-06 Score=74.58 Aligned_cols=61 Identities=20% Similarity=0.333 Sum_probs=50.3
Q ss_pred CcccceeeCCcchHHHHHhHhCCEEEEeCCCCC-----------------CCccEEEEEeC---HHHHHHHHHHHHHHHh
Q 009173 478 NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLG-----------------STDRIVVISGT---PDETQAAQSLLQAFIL 537 (541)
Q Consensus 478 ~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~-----------------s~~RiItIsGt---peqV~~Aq~LI~~~I~ 537 (541)
+++|.|||++|++||+|+++|||+|.|...... ...-.|.|++. .+.+++|..+|+.++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 789999999999999999999999999753110 12257889995 5899999999999886
Q ss_pred c
Q 009173 538 T 538 (541)
Q Consensus 538 ~ 538 (541)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 35
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.12 E-value=5.4e-06 Score=95.23 Aligned_cols=142 Identities=15% Similarity=0.271 Sum_probs=107.1
Q ss_pred CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT 263 (541)
Q Consensus 184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~ 263 (541)
..+...+-+-...+..|+||+|.+|.+|+++++|.|.+.. .+..+..+.++|..... ..+.+.+..++..+..
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~---~ka~~~v~~~~~ei~n-- 417 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSAND---EKAVEDVEKIIAEILN-- 417 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccch---hHHHHHHHHHHHhhhc--
Confidence 3467778888999999999999999999999999999986 45677889999975542 2233334333333221
Q ss_pred cccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccC-eeEEEccCcccccCCCCCceEEEEcCHHHHHHHH
Q 009173 264 SEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG-TSIRIISDQLLKCISENDRVVQISGEFSKVKDAV 342 (541)
Q Consensus 264 ~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TG-A~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~ 342 (541)
+.+...+.+|...+..+||.+|..|++|..++| .+|+...+. +....+++.|....+..+.
T Consensus 418 ------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------~~~~~~~~~~~~~dv~~~~ 479 (753)
T KOG2208|consen 418 ------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------NSSDMVTIRGISKDVEKSV 479 (753)
T ss_pred ------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC------cccccceEeccccccchhH
Confidence 134557899999999999999999999999999 666665332 2345588899988888877
Q ss_pred HHHHHHhh
Q 009173 343 YNVTGRLR 350 (541)
Q Consensus 343 ~lI~~~l~ 350 (541)
.+...+..
T Consensus 480 ~~~~~~~~ 487 (753)
T KOG2208|consen 480 SLLKALKA 487 (753)
T ss_pred HHHHhhhh
Confidence 77766654
No 36
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.05 E-value=7e-06 Score=73.54 Aligned_cols=66 Identities=29% Similarity=0.363 Sum_probs=50.9
Q ss_pred ccccccccccccchhhhhhcccCeeEEEccCc-c-----------cccCCCCC-ceEEEEcCH---HHHHHHHHHHHHHh
Q 009173 286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQ-L-----------LKCISEND-RVVQISGEF---SKVKDAVYNVTGRL 349 (541)
Q Consensus 286 ~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~-~-----------P~~~~s~e-rvVtItGt~---e~V~~A~~lI~~~l 349 (541)
-+++|.|||++|.+||+|+++|||+|.|..+. . |..+..++ -.|.|++.. +++.+|+.+|..++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 35789999999999999999999999998431 0 11111122 349999965 99999999999999
Q ss_pred hc
Q 009173 350 RD 351 (541)
Q Consensus 350 ~e 351 (541)
.+
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 74
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.02 E-value=8.3e-06 Score=82.21 Aligned_cols=150 Identities=21% Similarity=0.343 Sum_probs=107.7
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcccc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF 354 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~~~ 354 (541)
...++..+.||..+++.+.|++|.+||.|+.+|...|+-+.. ..+.++.++|..+.|..|++.|...-.....
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr-------~eePiF~vTg~~edv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR-------GEEPIFPVTGRHEDVRRARREIPSAAEHFGL 95 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCC-------CCCCcceeccCchhHHHHhhcCccccceeee
Confidence 367888999999999999999999999999999999988721 2345799999999999998776543311000
Q ss_pred CCCcccccccCCCCccccCCCCCCCCCCCccccccccccCCCCCCCCCccCCCccCCCCCCCCCCCCccccccccccccC
Q 009173 355 SGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHL 434 (541)
Q Consensus 355 ~~~~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~~~~~~r~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~g~~~ 434 (541)
.|.. +
T Consensus 96 -------------------------------------------~~~s-------------------~------------- 100 (394)
T KOG2113|consen 96 -------------------------------------------IRAS-------------------R------------- 100 (394)
T ss_pred -------------------------------------------eeec-------------------c-------------
Confidence 0000 0
Q ss_pred CCCCCCCCCCcCCCCCCCCCcccCCCCCcccccceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCcc
Q 009173 435 RGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDR 514 (541)
Q Consensus 435 ~g~~d~~~~~~~g~~~~~~~l~~~sg~~~a~~~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~R 514 (541)
.++ .|.+... ...+++.++.+|...+|.|.|..|.+|+.|++.+...|.-.- ...+-
T Consensus 101 ----s~S----gg~~~~s------------~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v---~~~~~ 157 (394)
T KOG2113|consen 101 ----SFS----GGTNGAS------------ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV---RCGEP 157 (394)
T ss_pred ----ccc----CCCcccc------------ccCCCceeeeccceeeeeccccccCccchheecccceEeeec---cCCCc
Confidence 000 0000000 012467789999999999999999999999999988877642 23567
Q ss_pred EEEEEeCHHH-HHHHH
Q 009173 515 IVVISGTPDE-TQAAQ 529 (541)
Q Consensus 515 iItIsGtpeq-V~~Aq 529 (541)
++-++|-+.. +++|.
T Consensus 158 Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 158 VFCVTGAPKNCVKRAR 173 (394)
T ss_pred eEEEecCCcchhhhcc
Confidence 8999998887 56665
No 38
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.85 E-value=1e-05 Score=81.62 Aligned_cols=146 Identities=20% Similarity=0.274 Sum_probs=104.2
Q ss_pred CceEEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc
Q 009173 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT 263 (541)
Q Consensus 184 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~ 263 (541)
+.++..+-+|...++.|.|++|.+||.|+.+|...|+-+. -..|-++.++|..+. +..|...+... .+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPs---r~eePiF~vTg~~ed------v~~aRrei~sa--aeH 92 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPS---RGEEPIFPVTGRHED------VRRARREIPSA--AEH 92 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCC---CCCCCcceeccCchh------HHHHhhcCccc--cce
Confidence 5688889999999999999999999999999999998762 234567888998664 44444443320 011
Q ss_pred c---------ccCCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcC
Q 009173 264 S---------EKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334 (541)
Q Consensus 264 ~---------~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt 334 (541)
+ ..+. .+.......+...-+|-..+|.|.|..|.+|+.|++.+...|.-+.. ..+.++.++|.
T Consensus 93 ~~l~~~s~s~Sgg~-~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-------~~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 93 FGLIRASRSFSGGT-NGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-------CGEPVFCVTGA 164 (394)
T ss_pred eeeeeecccccCCC-ccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-------CCCceEEEecC
Confidence 1 0111 11112334456778899999999999999999999999999887621 24678999999
Q ss_pred HHH-HHHHH-HHHHHH
Q 009173 335 FSK-VKDAV-YNVTGR 348 (541)
Q Consensus 335 ~e~-V~~A~-~lI~~~ 348 (541)
+.+ +++|. ..|+..
T Consensus 165 ~~nC~kra~s~eie~t 180 (394)
T KOG2113|consen 165 PKNCVKRARSCEIEQT 180 (394)
T ss_pred Ccchhhhccccchhhh
Confidence 988 55565 444443
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.84 E-value=2.1e-05 Score=72.38 Aligned_cols=102 Identities=20% Similarity=0.325 Sum_probs=69.5
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~ 266 (541)
.+.++|+...+|+.||++|++|+.|++..|-+|.|-. -+ ++ ..+-+..++.. ....
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~s--~d-------~~~fI~n~l~P---a~V~- 88 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------YS--DD-------PEEFIKNIFAP---AAVR- 88 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------cC--CC-------HHHHHHHHcCC---CEEE-
Confidence 6678899999999999999999999999998888742 11 11 12222222111 0000
Q ss_pred CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEE
Q 009173 267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (541)
Q Consensus 267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I 313 (541)
.... ...+....+.+.|+....|..|||+|++++.++..+|-.+.|
T Consensus 89 ~v~I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 89 SVTI-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEEE-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 0000 001223456788999999999999999999999999887766
No 40
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.49 E-value=0.00028 Score=80.11 Aligned_cols=66 Identities=18% Similarity=0.275 Sum_probs=58.0
Q ss_pred ceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
......+.||.+++|.|||+||++||+|+++||++|.|. .+..|.|.+ +.+++++|+.+|..+...
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~----------d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE----------DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe----------cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 345678999999999999999999999999999999994 356788888 678999999999998863
No 41
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.46 E-value=0.00027 Score=80.21 Aligned_cols=62 Identities=23% Similarity=0.455 Sum_probs=56.5
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL 537 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~ 537 (541)
...+.||.+++|.|||.||.+||.|.++|||+|.|.+ +..|.|.+ +.+++++|+.+|+..+.
T Consensus 579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 5688999999999999999999999999999999976 37788888 58899999999998876
No 42
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.45 E-value=0.00025 Score=65.33 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=33.5
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
....+.|+.+..|..|||+|.||+.+++.+|-++.|.
T Consensus 99 ~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 99 KVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 3567889999999999999999999999999998874
No 43
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.36 E-value=0.00076 Score=72.16 Aligned_cols=75 Identities=23% Similarity=0.352 Sum_probs=57.8
Q ss_pred eeEEEEEec------ccccccccccccchhhhhhcccCeeEEEcc-----Cc------ccccCCCCCce-EEEEc-CHHH
Q 009173 277 LVNARLVVA------SNQVGCLLGKGGTIISEMRKVTGTSIRIIS-----DQ------LLKCISENDRV-VQISG-EFSK 337 (541)
Q Consensus 277 ~vt~~l~VP------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~-----d~------~P~~~~s~erv-VtItG-t~e~ 337 (541)
.++-++.|| -++||+|||..|.|.|+|+++|||+|.|-+ |. +.......|.+ +.|++ +.++
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 566788888 468999999999999999999999999973 11 11111244555 88887 5678
Q ss_pred HHHHHHHHHHHhhc
Q 009173 338 VKDAVYNVTGRLRD 351 (541)
Q Consensus 338 V~~A~~lI~~~l~e 351 (541)
|++|+.+|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999976
No 44
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.25 E-value=0.00037 Score=64.15 Aligned_cols=102 Identities=21% Similarity=0.271 Sum_probs=68.1
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~ 266 (541)
.+-++|....+|+.||++|++|+.|++..|=+|.|-. -+. ++ ..-+...+ .......
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe-----------ys~--D~-------~~fI~N~l---~PA~V~~ 90 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE-----------YSE--NL-------EEFVANKL---APAEVKN 90 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE-----------cCC--CH-------HHHHHHcC---CCceEEE
Confidence 6668889999999999999999999988888887642 111 11 11111111 0000000
Q ss_pred CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEE
Q 009173 267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (541)
Q Consensus 267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I 313 (541)
... ...+......+.||.+..+..|||+|.+++...+.+|-++.|
T Consensus 91 -V~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 91 -VTV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred -EEE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 000 001223457788999999999999999999999999887766
No 45
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.07 E-value=0.001 Score=76.25 Aligned_cols=65 Identities=22% Similarity=0.382 Sum_probs=55.4
Q ss_pred eeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
.....+.||.+++|.|||+||++||+|+++|||+|.|. .+..|.|.+ ..+.+.+|..+|..+..+
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE----------DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 45678999999999999999999999999999999994 245677776 677899999999888753
No 46
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.99 E-value=0.0011 Score=75.89 Aligned_cols=63 Identities=21% Similarity=0.341 Sum_probs=54.6
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL 537 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~ 537 (541)
....+.||.+++|.|||+||.+||.|.++|||+|.|.+ +..|.|.+ ..+.+++|+..|.....
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 35788999999999999999999999999999999975 25677766 57889999999988764
No 47
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=96.89 E-value=0.0017 Score=59.82 Aligned_cols=37 Identities=16% Similarity=0.239 Sum_probs=33.4
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
....+.||.+..+..|||+|.|++..++.+|-++.|.
T Consensus 100 ~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 100 KVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 3568899999999999999999999999999998774
No 48
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.86 E-value=0.0019 Score=68.09 Aligned_cols=66 Identities=15% Similarity=0.221 Sum_probs=55.3
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFIL 537 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~ 537 (541)
....+.|-.++||.|||+||++|++|+..|.++|+|.... .+-.|+|-|...--.+|+..|..++.
T Consensus 47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhhh
Confidence 3457788899999999999999999999999999997533 35789999998877888887776653
No 49
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.70 E-value=0.0039 Score=69.21 Aligned_cols=68 Identities=25% Similarity=0.517 Sum_probs=59.3
Q ss_pred ceEEEEEecc-CcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173 468 NTTVEIIVPE-NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP 540 (541)
Q Consensus 468 ~~t~~V~IP~-~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~ 540 (541)
.++..|.+|+ ++-|+|||+.|.||+.+...||++|.|++.+ ..|+||| +|---+.|+..|...|..|+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~dgr 272 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQDGR 272 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHHcCC
Confidence 4677889999 5669999999999999999999999997642 5688999 78888999999999998875
No 50
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.70 E-value=0.0044 Score=59.87 Aligned_cols=102 Identities=27% Similarity=0.314 Sum_probs=67.9
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhccccc
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~ 266 (541)
.+-+.+-.+.+|..||++|++|+.|+++.|=+|.|-. -++++ ..-+..++....-....
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe-------------~s~d~-------~~fI~nal~Pa~v~~V~- 135 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE-------------WSEDP-------AEFIKNALAPAEVLSVN- 135 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE-------------eCCCH-------HHHHHHhcCcceEeEEE-
Confidence 3445556677999999999999999999996666532 22232 11111122100000000
Q ss_pred CCCCCCCCCceeEEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173 267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (541)
Q Consensus 267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~ 314 (541)
.. ..+.. ...+.||.++.+..|||+|.+++-..+.||-++.|.
T Consensus 136 ---~~-~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 136 ---IK-EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred ---EE-eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 00 00112 678889999999999999999999999999999996
No 51
>PRK00106 hypothetical protein; Provisional
Probab=96.65 E-value=0.005 Score=68.29 Aligned_cols=68 Identities=29% Similarity=0.581 Sum_probs=59.6
Q ss_pred ceEEEEEecc-CcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173 468 NTTVEIIVPE-NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP 540 (541)
Q Consensus 468 ~~t~~V~IP~-~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~ 540 (541)
.++..|.+|+ ++-|+|||+.|.||+.+...||+++.|++.+ ..|+||| +|---+.|+..|...|..|+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~dgr 293 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKDGR 293 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence 4667889999 5669999999999999999999999997643 5688999 89999999999999998875
No 52
>PRK12704 phosphodiesterase; Provisional
Probab=96.49 E-value=0.0069 Score=67.38 Aligned_cols=68 Identities=24% Similarity=0.506 Sum_probs=57.1
Q ss_pred ceEEEEEecc-CcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173 468 NTTVEIIVPE-NVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP 540 (541)
Q Consensus 468 ~~t~~V~IP~-~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~ 540 (541)
.++..|.+|+ ++-|+|||+.|.||+.+...||++|.|++. ...|+||| +|---+.|+..|...+..|.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~~~~~rre~a~~~l~~l~~dg~ 278 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPIRREIARLALEKLVQDGR 278 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEecCChhhHHHHHHHHHHHHhcCC
Confidence 4667889998 566999999999999999999999999764 26788999 67777888888888877653
No 53
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.47 E-value=0.0029 Score=66.75 Aligned_cols=68 Identities=26% Similarity=0.295 Sum_probs=55.7
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHh
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL 349 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l 349 (541)
.......+.|-+++||.|||+||++|+.||..|+++|+|.+. ..+-.|+|-|...--.+|...|...+
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~-------~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC-------DLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc-------CceeEEEEechHHHHHHHHhhHhhhh
Confidence 345667888999999999999999999999999999999743 34678999999887667766665444
No 54
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.43 E-value=0.0032 Score=62.96 Aligned_cols=41 Identities=22% Similarity=0.438 Sum_probs=36.6
Q ss_pred CCceEEEEEeccc------cccceeccCchHHHHHHHHhCCeEEecC
Q 009173 183 QQEVSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVGA 223 (541)
Q Consensus 183 ~~~~~~rilvP~~------~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~ 223 (541)
.-.++.|++||.+ +||.|+|.+|.++|+|+++|||+|.|-.
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 3457889999988 6999999999999999999999999863
No 55
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.41 E-value=0.0051 Score=48.45 Aligned_cols=36 Identities=31% Similarity=0.541 Sum_probs=33.9
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCeEEe
Q 009173 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (541)
Q Consensus 186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I 221 (541)
..+.+.|+.+.+|..|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 688899999999999999999999999999988876
No 56
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.37 E-value=0.0048 Score=71.80 Aligned_cols=66 Identities=18% Similarity=0.292 Sum_probs=56.9
Q ss_pred ceeEEEEEecccccccccccccchhhhhhcccCee-EEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS-IRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 276 ~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~-I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
......+.||.+++|.|||.||.+||+|.++||++ |.+. .+-.|.|.+ +.+++++|+.+|.++..+
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 34567899999999999999999999999999999 8773 246788888 788999999999998764
No 57
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.36 E-value=0.005 Score=48.49 Aligned_cols=36 Identities=22% Similarity=0.528 Sum_probs=33.7
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEE
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV 504 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I 504 (541)
....+.||.+..|.+|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 468999999999999999999999999999988876
No 58
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.35 E-value=0.0077 Score=64.70 Aligned_cols=61 Identities=23% Similarity=0.421 Sum_probs=48.5
Q ss_pred CcccceeeCCcchHHHHHhHhCCEEEEeC------CC---------CCCCc-cEEEEEe-CHHHHHHHHHHHHHHHhc
Q 009173 478 NVIGSVYGENGSNLLRLRQISGAKVIVHE------PR---------LGSTD-RIVVISG-TPDETQAAQSLLQAFILT 538 (541)
Q Consensus 478 ~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~------p~---------~~s~~-RiItIsG-tpeqV~~Aq~LI~~~I~~ 538 (541)
+++|+|||..|.|.|+|.++|||+|.|-- -+ +...+ =-+.|++ |.|.|++|..+|+.+|.+
T Consensus 153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 69999999999999999999999999962 01 11122 2467777 577899999999999975
No 59
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.04 E-value=0.0059 Score=71.07 Aligned_cols=63 Identities=11% Similarity=0.266 Sum_probs=55.6
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCE-EEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAK-VIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL 537 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~-I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~ 537 (541)
....+.||.+++|.|||.||.+|+.|.++||+. |.|.+ +-.|.|.+ +.+.+++|+.+|.+...
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 467889999999999999999999999999999 99865 36688887 58899999999998865
No 60
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.01 E-value=0.0093 Score=61.38 Aligned_cols=68 Identities=16% Similarity=0.260 Sum_probs=56.6
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhc
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILT 538 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~ 538 (541)
....+.++..+.|.|||+.|.+.+.|+++|+++|.++. +.++...|+|+| ..++|.+|...|.-+|-+
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~--p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR--PNTNKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC--CCCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 34577899999999999999999999999999999954 454555566655 688999999999888865
No 61
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.92 E-value=0.011 Score=66.34 Aligned_cols=64 Identities=19% Similarity=0.328 Sum_probs=56.3
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCH-HHHHHHHHHHHHHHhc
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTP-DETQAAQSLLQAFILT 538 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtp-eqV~~Aq~LI~~~I~~ 538 (541)
...++.|+.++++-|||+||.+|++|.++|||+|.|.+ +..|.|.++. +.+++|+..|.++...
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 56788999999999999999999999999999999963 3568898875 7899999999998753
No 62
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.87 E-value=0.019 Score=64.47 Aligned_cols=66 Identities=21% Similarity=0.330 Sum_probs=57.5
Q ss_pred eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCH-HHHHHHHHHHHHHhhccc
Q 009173 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEF-SKVKDAVYNVTGRLRDNH 353 (541)
Q Consensus 278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~-e~V~~A~~lI~~~l~e~~ 353 (541)
-...+.|+.+.++-+||+||++|++|.++|||+|.|. .+..|.|.++. +.+.+|+..|..+.++-.
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------DDGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 3567889999999999999999999999999999994 35678899876 788899999999997644
No 63
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.70 E-value=0.021 Score=57.22 Aligned_cols=60 Identities=18% Similarity=0.314 Sum_probs=52.2
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGT-PDETQAAQSLLQAFI 536 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGt-peqV~~Aq~LI~~~I 536 (541)
+.+.||.++++.+||++|.+|+.|.+.++++|.|.. +..|-|+|+ .+.+++|+.+|+..=
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~e 207 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKIE 207 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHHH
Confidence 578999999999999999999999999999999964 367888886 668999999998653
No 64
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.56 E-value=0.015 Score=67.07 Aligned_cols=64 Identities=22% Similarity=0.369 Sum_probs=54.0
Q ss_pred eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
....+.||.+.++.+||.||.+||+|.++||++|.+. .+..|.|.+ ..+++.+|..+|..+..+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 4457778999999999999999999999999988772 246788888 678899999999888754
No 65
>PRK00468 hypothetical protein; Provisional
Probab=95.37 E-value=0.018 Score=47.33 Aligned_cols=34 Identities=29% Similarity=0.534 Sum_probs=30.2
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHh
Q 009173 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (541)
Q Consensus 182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eT 215 (541)
....+.+++.|..+.+|.||||+|.+|+.|+.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 4456899999999999999999999999998754
No 66
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.30 E-value=0.042 Score=57.99 Aligned_cols=94 Identities=27% Similarity=0.386 Sum_probs=62.0
Q ss_pred cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173 196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK 274 (541)
Q Consensus 196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~ 274 (541)
-+|+.||++|++|+.|.++. |=+|.|-. =++++ .. .+..-+.......- .. .+.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~-------~~---fi~nal~Pa~v~~v-~i-~~~ 298 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIE-------------YSDDP-------AE---FIANALSPAKVISV-EV-LDE 298 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEE-------------cCCCH-------HH---HHHHhcCCceEEEE-EE-EcC
Confidence 48999999999999999998 66776632 11121 00 11110100000000 00 001
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~ 315 (541)
....+.+.||.++.+..|||+|.+++-..+.||.+|.|..
T Consensus 299 -~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 -DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred -CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 1236789999999999999999999999999999999963
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.22 E-value=0.031 Score=59.18 Aligned_cols=92 Identities=24% Similarity=0.254 Sum_probs=61.6
Q ss_pred cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173 196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK 274 (541)
Q Consensus 196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~ 274 (541)
-+|+.||++|++|+.|.++. |=+|.|-. =++++ .. .+..-+.......- .. .
T Consensus 252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~-------------~s~D~-------~~---fI~Nal~Pa~V~~V-~i--~- 304 (374)
T PRK12328 252 PIGATVGVKGVRINAVSKELNGENIDCIE-------------YSNVP-------EI---FIARALAPAIISSV-KI--E- 304 (374)
T ss_pred hHHhhcCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH-------HH---HHHHhCCCceeeEE-EE--c-
Confidence 48999999999999999998 66666532 11221 11 11111110000000 00 0
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~ 314 (541)
...-...+.||..+.+..|||+|.+++-..+.||.+|.|.
T Consensus 305 ~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 305 EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 1123678899999999999999999999999999999998
No 68
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.19 E-value=0.03 Score=54.07 Aligned_cols=37 Identities=35% Similarity=0.592 Sum_probs=31.8
Q ss_pred eEEEEEec------cCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 469 TTVEIIVP------ENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP------~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
.+-.+.|| .++||.+||..|+++|+++..|+|+|-|-
T Consensus 148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR 190 (269)
T COG5176 148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR 190 (269)
T ss_pred ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence 44556665 37999999999999999999999999995
No 69
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.18 E-value=0.02 Score=58.94 Aligned_cols=69 Identities=20% Similarity=0.277 Sum_probs=56.1
Q ss_pred eEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE-cCHHHHHHHHHHHHHHhhcc
Q 009173 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-GEFSKVKDAVYNVTGRLRDN 352 (541)
Q Consensus 278 vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt-Gt~e~V~~A~~lI~~~l~e~ 352 (541)
....+.|++...|.|||++|.|.++|+++|+++|.+++- . ++...++|+ +..++|.+|...|...|.+.
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p---~---~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP---N---TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC---C---CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 456788999999999999999999999999999999732 1 233444444 57889999999999988654
No 70
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.08 E-value=0.039 Score=55.27 Aligned_cols=64 Identities=20% Similarity=0.292 Sum_probs=53.7
Q ss_pred EEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHH-HHHHHHHHHHHHhhccc
Q 009173 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS-KVKDAVYNVTGRLRDNH 353 (541)
Q Consensus 280 ~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e-~V~~A~~lI~~~l~e~~ 353 (541)
+.+.||.++++.+||++|.+|+.|.+.++++|.+- .+-.|.|.|... ++.+|..+|..+-++..
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------QNGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 56889999999999999999999999999999882 245788888655 88888888888776554
No 71
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.08 E-value=0.029 Score=56.24 Aligned_cols=38 Identities=32% Similarity=0.691 Sum_probs=33.8
Q ss_pred ceEEEEEecc------CcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 468 NTTVEIIVPE------NVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 468 ~~t~~V~IP~------~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
..+.+|.||- ++||+|+|..|.++|+|+++|||+|-|-
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 3567788874 5999999999999999999999999995
No 72
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=95.07 E-value=0.0079 Score=69.92 Aligned_cols=70 Identities=21% Similarity=0.179 Sum_probs=60.1
Q ss_pred cceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC-CCCCCCccEEEEEeCHHHHHHHHHHHHHHH
Q 009173 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE-PRLGSTDRIVVISGTPDETQAAQSLLQAFI 536 (541)
Q Consensus 467 ~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~-p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I 536 (541)
......+.+|.+...+|||+||+||+.+|..+||.|+|.+ -.....+|.+++.|.|+.+..|-.+|...|
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence 3455678899999999999999999999999999999986 233467999999999999999998886554
No 73
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.00 E-value=0.051 Score=57.73 Aligned_cols=94 Identities=28% Similarity=0.295 Sum_probs=62.3
Q ss_pred cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173 196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK 274 (541)
Q Consensus 196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~ 274 (541)
-+|+.||++|++|+.|.++. |=+|.|-. =++++ ..- +..-+.......- .- . .
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~-------------~s~d~-------~~f---i~nal~Pa~v~~v-~i-~-~ 299 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIID-------------WSEDP-------AEF---VANALSPAKVVSV-EV-D-D 299 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEE-------------cCCCH-------HHH---HHHhCCCceEEEE-EE-E-c
Confidence 48999999999999999998 76777632 11121 111 1111110000000 00 0 0
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~ 315 (541)
.....+.+.||.++.+..|||+|.+++--...||.+|.|..
T Consensus 300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 11236789999999999999999999999999999999973
No 74
>PRK02821 hypothetical protein; Provisional
Probab=94.99 E-value=0.024 Score=46.79 Aligned_cols=36 Identities=28% Similarity=0.523 Sum_probs=30.9
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhCC
Q 009173 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (541)
Q Consensus 182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa 217 (541)
....+.+.|.|..+.+|.||||+|.+|+.|+.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 344578999999999999999999999999987543
No 75
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.82 E-value=0.052 Score=59.61 Aligned_cols=93 Identities=27% Similarity=0.384 Sum_probs=62.0
Q ss_pred cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173 196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK 274 (541)
Q Consensus 196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~ 274 (541)
-+|+.||++|++|+.|.++. |=+|.|-. =++++ ...+..-+.......-. .+.
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~pa~v~~v~---~~~ 299 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIIL-------------WSDDP----------AQFIINALSPAEVSSVV---VDE 299 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCCEEEEEE---EeC
Confidence 38999999999999999998 66776632 11121 01111111110000000 000
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~ 315 (541)
..-.+.+.||..+.+..|||+|.+++-..+.||.+|.|..
T Consensus 300 -~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 300 -DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred -CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 1136789999999999999999999999999999999973
No 76
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.74 E-value=0.83 Score=44.63 Aligned_cols=63 Identities=16% Similarity=0.259 Sum_probs=53.4
Q ss_pred EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhh
Q 009173 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR 350 (541)
Q Consensus 279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~ 350 (541)
.+.+.++....-.++..+|..+++|-...||+|.+..+ +..+.|+|+...+..+...|.+.+.
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~---------~~~i~I~g~k~~~~~i~~~i~~~l~ 89 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS---------ENRIRITGTKSTAEYIEASINEILS 89 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC---------CcEEEEEccHHHHHHHHHHHHHHHh
Confidence 34555568888999999999999998888999999633 5689999999999999999888885
No 77
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.72 E-value=0.048 Score=58.80 Aligned_cols=93 Identities=27% Similarity=0.329 Sum_probs=61.0
Q ss_pred cccceeccCchHHHHHHHHh-CCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCC
Q 009173 196 KVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNK 274 (541)
Q Consensus 196 ~vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~ 274 (541)
-+|+.||++|++|+.|.++. |=+|.|-. =++++ .. .|..-+........ .. .+
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~-------------ys~Dp-------~~---fI~NaLsPA~V~~V-~i-~~- 331 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIR-------------WSPDP-------AT---YIANALSPARVDEV-RL-VD- 331 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH-------HH---HHHHhcCCceeeEE-EE-Ec-
Confidence 48999999999999999998 66666532 11221 11 11111100000000 00 00
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~ 314 (541)
.....+.+.||.++.+..|||+|.+++--...||.+|.|.
T Consensus 332 ~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 332 PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 1123568999999999999999999999999999999885
No 78
>PRK12705 hypothetical protein; Provisional
Probab=94.72 E-value=0.039 Score=61.03 Aligned_cols=68 Identities=22% Similarity=0.458 Sum_probs=54.9
Q ss_pred ceEEEEEeccC-cccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcCC
Q 009173 468 NTTVEIIVPEN-VIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTGP 540 (541)
Q Consensus 468 ~~t~~V~IP~~-~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~~ 540 (541)
.++..|.+|++ +-|+|||+.|.||+.+...||+.|.|++-+ ..|+|++ .|.--+.|+..+...|..|+
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~fdp~rreia~~~l~~Li~dgr 266 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSFNPIRREIARLTLEKLLADGR 266 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhcccCccchHHHHHHHHHHHhcCC
Confidence 35678889985 559999999999999999999999997643 4477777 47777788888888877664
No 79
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=94.68 E-value=0.049 Score=52.72 Aligned_cols=37 Identities=19% Similarity=0.398 Sum_probs=34.4
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
...+.||.+..+.+|||+|.|++.+.+.||-++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 5688899999999999999999999999999999963
No 80
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.65 E-value=0.089 Score=58.57 Aligned_cols=64 Identities=20% Similarity=0.322 Sum_probs=49.3
Q ss_pred EEEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 279 t~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
+..+.+|+ ++-|+||||.|.+|+-++..||+++.| |+.| ..|+|+| +|---+-|...+..++.|
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~ii--ddtp-------~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--DDTP-------EAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEE--cCCC-------CeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34567887 567999999999999999999999999 5444 4677888 565556676666666654
No 81
>PRK12704 phosphodiesterase; Provisional
Probab=94.64 E-value=0.083 Score=58.89 Aligned_cols=64 Identities=20% Similarity=0.314 Sum_probs=48.3
Q ss_pred EEEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 279 t~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
+..+.+|+ ++-|+||||.|.+|+-++..||++|.| |+.| ..|.|+| ++---+.|...+...+.|
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~ii--ddtp-------~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--DDTP-------EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEE--cCCC-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 33566787 677999999999999999999999999 5444 4788998 555544566666665544
No 82
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.44 E-value=0.03 Score=64.50 Aligned_cols=62 Identities=23% Similarity=0.399 Sum_probs=53.0
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHh
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFIL 537 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~ 537 (541)
...+.||.++++.+||.||.+|+.|.++||++|.|.+ +..|.|.+ ..+.+++|+.+|+....
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhcc
Confidence 3567779999999999999999999999999888844 36688888 58889999999998764
No 83
>PRK00106 hypothetical protein; Provisional
Probab=94.37 E-value=0.12 Score=57.54 Aligned_cols=64 Identities=23% Similarity=0.371 Sum_probs=49.7
Q ss_pred EEEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 279 t~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
+..+.+|+ ++-|+||||.|.+|+-+...||+++.| |+.| ..|.|+| +|---+-|...+..++.|
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdlii--ddtp-------~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVII--DDTP-------EVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEE--cCCC-------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34567887 677999999999999999999999999 5444 4688888 666666676666666654
No 84
>PRK00468 hypothetical protein; Provisional
Probab=94.29 E-value=0.037 Score=45.53 Aligned_cols=32 Identities=34% Similarity=0.468 Sum_probs=28.6
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV 306 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~ 306 (541)
+..+.+++.+..+.+|+||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 45578899999999999999999999999974
No 85
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.26 E-value=0.051 Score=44.69 Aligned_cols=33 Identities=27% Similarity=0.535 Sum_probs=29.8
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHh
Q 009173 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (541)
Q Consensus 183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eT 215 (541)
...+.++|.+..+.+|.||||+|.+|+.|+.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 567899999999999999999999999999753
No 86
>PRK01064 hypothetical protein; Provisional
Probab=94.03 E-value=0.056 Score=44.82 Aligned_cols=34 Identities=21% Similarity=0.513 Sum_probs=30.4
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHh
Q 009173 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (541)
Q Consensus 182 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eT 215 (541)
....+.+++.|..+..|.+|||+|.+|+.|+.-.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 3567899999999999999999999999999853
No 87
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.91 E-value=0.049 Score=44.81 Aligned_cols=32 Identities=31% Similarity=0.493 Sum_probs=29.0
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV 306 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~ 306 (541)
+....+++.+..+.+|.||||+|.+|+.||--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 55778999999999999999999999999964
No 88
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.82 E-value=0.16 Score=49.14 Aligned_cols=40 Identities=23% Similarity=0.437 Sum_probs=34.4
Q ss_pred CceeEEEEEec------ccccccccccccchhhhhhcccCeeEEEc
Q 009173 275 GLLVNARLVVA------SNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (541)
Q Consensus 275 ~~~vt~~l~VP------~~~vG~IIGKgG~tIkeIr~~TGA~I~I~ 314 (541)
...++-++.|| .++||.|||..|.|.|+|++.|+|+|.|-
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR 190 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR 190 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence 34556677777 57899999999999999999999999997
No 89
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.82 E-value=1 Score=44.02 Aligned_cols=126 Identities=16% Similarity=0.178 Sum_probs=84.7
Q ss_pred EEeccccccceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCC
Q 009173 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLD 269 (541)
Q Consensus 190 ilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~ 269 (541)
+.++....-.+...+|..++.|-...||+|.+. .++..+.|+|++. ..+.+...+.++...
T Consensus 30 v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~-----~~~~~i~I~g~k~-------~~~~i~~~i~~~l~~------- 90 (210)
T PF14611_consen 30 VWLQPDEFFLLLTGNGRILENLAARNGAKIEVS-----RSENRIRITGTKS-------TAEYIEASINEILSN------- 90 (210)
T ss_pred EEecchheeeeecCCchHHHHHHHhcCceEEEe-----cCCcEEEEEccHH-------HHHHHHHHHHHHHhh-------
Confidence 333577788899999999999988889999997 4667899999765 444554444444432
Q ss_pred CCCCCCceeEEEEEeccccccccc----ccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEE-----cCHHHHHH
Q 009173 270 FSSNKGLLVNARLVVASNQVGCLL----GKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-----GEFSKVKD 340 (541)
Q Consensus 270 ~~~~~~~~vt~~l~VP~~~vG~II----GKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtIt-----Gt~e~V~~ 340 (541)
..+..+.++.-.--.-. -.....++.|++.|++.|+...+ +..+.|+ -....+..
T Consensus 91 -------i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~---------~~~~~i~~~~~~~~~~~~~~ 154 (210)
T PF14611_consen 91 -------IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD---------GNKLKISWLASPENEKRADR 154 (210)
T ss_pred -------cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC---------CCeEEEEEEeeccccchHHH
Confidence 22344444422111111 11356789999999999998633 2344454 46678888
Q ss_pred HHHHHHHHhh
Q 009173 341 AVYNVTGRLR 350 (541)
Q Consensus 341 A~~lI~~~l~ 350 (541)
|.+++.-.+.
T Consensus 155 a~RlL~~a~~ 164 (210)
T PF14611_consen 155 AKRLLLWALD 164 (210)
T ss_pred HHHHHHHhcc
Confidence 9999888874
No 90
>PRK02821 hypothetical protein; Provisional
Probab=92.97 E-value=0.083 Score=43.68 Aligned_cols=32 Identities=31% Similarity=0.486 Sum_probs=28.8
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCC
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGA 500 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA 500 (541)
...++.+...-+|+||||+|.+|+.||..-.|
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 57899999999999999999999999987654
No 91
>PRK01064 hypothetical protein; Provisional
Probab=92.30 E-value=0.12 Score=42.78 Aligned_cols=32 Identities=28% Similarity=0.466 Sum_probs=28.8
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV 306 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~ 306 (541)
...+.+++.|..+..|++|||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 45678899999999999999999999999975
No 92
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=91.77 E-value=0.29 Score=53.90 Aligned_cols=37 Identities=22% Similarity=0.511 Sum_probs=34.9
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
...+.||.+..+..|||+|.|++..++.||.+|.|..
T Consensus 303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 6789999999999999999999999999999999963
No 93
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=91.24 E-value=0.12 Score=41.96 Aligned_cols=35 Identities=26% Similarity=0.376 Sum_probs=29.2
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHhCC
Q 009173 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (541)
Q Consensus 183 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa 217 (541)
.....+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 34557788889999999999999999999976543
No 94
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=90.80 E-value=0.2 Score=48.29 Aligned_cols=54 Identities=30% Similarity=0.424 Sum_probs=48.9
Q ss_pred ccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhh
Q 009173 286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR 350 (541)
Q Consensus 286 ~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~ 350 (541)
+..+|+|+||+|.|---|++.|.++|.+. +..+-|-|..++++.|...|+.+|-
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec-----------CceEEEeecchhhHHHHHhhHhhhc
Confidence 55789999999999999999999999984 4578999999999999999999985
No 95
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.04 E-value=0.45 Score=36.94 Aligned_cols=35 Identities=34% Similarity=0.495 Sum_probs=28.6
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCeE
Q 009173 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219 (541)
Q Consensus 185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I 219 (541)
.....+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35666777776789999999999999999988443
No 96
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.84 E-value=0.33 Score=39.27 Aligned_cols=35 Identities=37% Similarity=0.547 Sum_probs=27.7
Q ss_pred EEEEecccc-----ccceeccCchHHHHHHHHh-CCeEEec
Q 009173 188 FRILCSNDK-----VGAVIGKGGTIIRALQSEA-GAFISVG 222 (541)
Q Consensus 188 ~rilvP~~~-----vG~IIGKgG~~Ik~Iq~eT-Ga~I~I~ 222 (541)
.++.|-+.. +|..||++|+.|+.|.++. |-+|+|-
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 456666666 9999999999999999999 8888764
No 97
>PRK12705 hypothetical protein; Provisional
Probab=88.71 E-value=0.72 Score=51.22 Aligned_cols=62 Identities=23% Similarity=0.282 Sum_probs=42.4
Q ss_pred EEEEecc-cccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhh
Q 009173 280 ARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLR 350 (541)
Q Consensus 280 ~~l~VP~-~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~ 350 (541)
..+.+|+ ++-|+||||.|.+|+.++..||+.+.| |+.|. .|.|.+ ++.--+.|...+..++.
T Consensus 200 s~v~lp~demkGriIGreGrNir~~E~~tGvdlii--ddtp~-------~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLII--DDTPE-------AVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred eeeecCChHhhccccCccchhHHHHHHhhCCceEe--cCCcc-------chhhcccCccchHHHHHHHHHHHh
Confidence 3456776 567999999999999999999999999 44443 455555 33333344444444443
No 98
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=88.00 E-value=0.53 Score=55.65 Aligned_cols=71 Identities=15% Similarity=0.124 Sum_probs=58.5
Q ss_pred EEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhcc
Q 009173 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352 (541)
Q Consensus 279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e~ 352 (541)
..++.+|-....+|||+||.+|+.++..|||-|.+.+- -|+ ...||.+.+.|.++.++.|...|.-.+.|-
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm-q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM-QPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhc-CCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence 34677888889999999999999999999999999631 111 146899999999999999988887777553
No 99
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=86.07 E-value=1.3 Score=34.38 Aligned_cols=34 Identities=24% Similarity=0.389 Sum_probs=27.0
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEE
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKV 502 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I 502 (541)
....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 3455666655689999999999999999998544
No 100
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=85.91 E-value=0.37 Score=39.05 Aligned_cols=33 Identities=15% Similarity=0.300 Sum_probs=27.9
Q ss_pred eeEEEEEecccccccccccccchhhhhhcccCe
Q 009173 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGT 309 (541)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA 309 (541)
...+.+.+..+..|.||||.|.+++.||--.++
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 346788889999999999999999999976543
No 101
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=85.32 E-value=0.46 Score=38.87 Aligned_cols=35 Identities=26% Similarity=0.370 Sum_probs=29.5
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCeEE
Q 009173 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS 220 (541)
Q Consensus 186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~ 220 (541)
....+.+.....|.|||++|++|+.|....+-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 35668889999999999999999999988765553
No 102
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=84.87 E-value=0.88 Score=37.32 Aligned_cols=34 Identities=32% Similarity=0.494 Sum_probs=26.9
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEE
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS 220 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~ 220 (541)
.+.+-+..+..|.+|||.|+++..||--+..-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 3445666788999999999999999988765444
No 103
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=84.27 E-value=0.86 Score=36.85 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=28.7
Q ss_pred EEEEEeccCc-----ccceeeCCcchHHHHHhHh-CCEEEEe
Q 009173 470 TVEIIVPENV-----IGSVYGENGSNLLRLRQIS-GAKVIVH 505 (541)
Q Consensus 470 t~~V~IP~~~-----vG~IIGkgGs~Ik~Irq~S-GA~I~I~ 505 (541)
...|.|-... +|..||++|++|+.|.++. |-+|.|-
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 3456666666 8999999999999999999 9999885
No 104
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=83.15 E-value=0.82 Score=44.19 Aligned_cols=56 Identities=16% Similarity=0.396 Sum_probs=50.1
Q ss_pred cCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhcC
Q 009173 477 ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILTG 539 (541)
Q Consensus 477 ~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~~ 539 (541)
+..+|+|+||+|.+--.|...|..+|.+.+ ..|-|-|+-+++..|+..|...|+..
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccC
Confidence 457899999999999999999999999954 56999999999999999999998753
No 105
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=83.09 E-value=0.49 Score=38.70 Aligned_cols=34 Identities=24% Similarity=0.441 Sum_probs=28.6
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEE
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKV 502 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I 502 (541)
....+.+-...-|.|||++|++|++|++..+-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4567888899999999999999999988775444
No 106
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=82.69 E-value=4.8 Score=44.72 Aligned_cols=66 Identities=21% Similarity=0.313 Sum_probs=54.8
Q ss_pred CceeEEEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEc-CHHHHHHHHHHHHHHhhc
Q 009173 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItG-t~e~V~~A~~lI~~~l~e 351 (541)
...+...+.|+.++...+||.+|...|+|..+||+.-.+ | +..++|.. +..+.++|++.|..++.+
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v--D---------e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV--D---------EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccceeee--c---------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 456677899999999999999999999999999965555 2 45677776 677888999999998865
No 107
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=79.89 E-value=1.3 Score=48.24 Aligned_cols=37 Identities=27% Similarity=0.418 Sum_probs=33.9
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEecC
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~ 223 (541)
...+.+|.+.++.+|||+|.+|++|+++.|-+|.|..
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 3557889999999999999999999999999999975
No 108
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.82 E-value=2 Score=35.85 Aligned_cols=36 Identities=22% Similarity=0.275 Sum_probs=30.0
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEec
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG 222 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~ 222 (541)
..++.+-...-|.|||++|+.|++|+++-.-...+.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 477888889999999999999999999876555443
No 109
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=79.49 E-value=3.5 Score=41.91 Aligned_cols=51 Identities=18% Similarity=0.303 Sum_probs=46.0
Q ss_pred cceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhc
Q 009173 481 GSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQAFILT 538 (541)
Q Consensus 481 G~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~~~I~~ 538 (541)
-++||.+|++++.|.-.|.|.|-|+- ..|.+.|.-..++.++..+.+++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 46899999999999999999999963 5689999999999999999999865
No 110
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=79.19 E-value=2.7 Score=39.85 Aligned_cols=35 Identities=31% Similarity=0.439 Sum_probs=29.7
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEec
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG 222 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~ 222 (541)
.+-++|-... |.-|||+|++|+++++..|-+|.+-
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 3446776666 9999999999999999999888875
No 111
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=78.29 E-value=2 Score=45.52 Aligned_cols=37 Identities=22% Similarity=0.485 Sum_probs=34.9
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
....+.||.+..+..|||+|.|++..++.||.+|.|.
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 3679999999999999999999999999999999996
No 112
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.13 E-value=6.3 Score=36.52 Aligned_cols=92 Identities=15% Similarity=0.446 Sum_probs=58.0
Q ss_pred eccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc-cCCCCCCCCCceeE
Q 009173 201 IGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE-KGLDFSSNKGLLVN 279 (541)
Q Consensus 201 IGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~-~g~~~~~~~~~~vt 279 (541)
+=..|..|++|-++-.-+|.|-.. ++ . +.+-.+|...|. +++....+ ....|.. .+
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~d--------------ps--~-l~~~e~A~~~I~-~ivP~ea~i~di~Fd~-----~t 77 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPD--------------PS--V-LKPPEEAIKIIL-EIVPEEAGITDIYFDD-----DT 77 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCC--------------hh--h-cCCHHHHHHHHH-HhCCCccCceeeEecC-----CC
Confidence 345678899999988888877521 10 0 001223444333 34422111 1111221 24
Q ss_pred EEEEecccccccccccccchhhhhhcccCeeEEEcc
Q 009173 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315 (541)
Q Consensus 280 ~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~ 315 (541)
-++.|-...-|.+|||+|.++++|..+||-.-++.+
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 477888889999999999999999999999888864
No 113
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=77.69 E-value=2.5 Score=34.67 Aligned_cols=34 Identities=26% Similarity=0.396 Sum_probs=27.5
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEE
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVI 503 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~ 503 (541)
...+.|..+..|.+|||.|.+++.|+-....-+.
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4567777788999999999999999988764433
No 114
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=76.50 E-value=2.5 Score=45.10 Aligned_cols=37 Identities=14% Similarity=0.252 Sum_probs=34.9
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
....+.||.+..+..|||+|.|++-.++.||.+|.|.
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 4678999999999999999999999999999999997
No 115
>PRK13764 ATPase; Provisional
Probab=76.31 E-value=2.2 Score=48.44 Aligned_cols=39 Identities=23% Similarity=0.440 Sum_probs=36.2
Q ss_pred cceEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 467 ~~~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
......|.||.+.++.+|||+|.+|++|.+..|.+|.|.
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~ 517 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVR 517 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEE
Confidence 346788999999999999999999999999999999997
No 116
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=76.26 E-value=5.5 Score=39.83 Aligned_cols=36 Identities=28% Similarity=0.479 Sum_probs=33.2
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
.-+.||..++.++||++|+.++-|.+.++|+|-|..
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 467899999999999999999999999999999963
No 117
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=76.19 E-value=3 Score=46.22 Aligned_cols=64 Identities=16% Similarity=0.183 Sum_probs=53.3
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHHhcC
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISG-TPDETQAAQSLLQAFILTG 539 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsG-tpeqV~~Aq~LI~~~I~~~ 539 (541)
....+.|+.++.-.+||.+|-+.|.|..+|||--.++ +..+.|-. ++..++.|+.+|...+...
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 4567888999999999999999999999999666553 35677766 5888999999999988653
No 118
>PRK13764 ATPase; Provisional
Probab=76.07 E-value=2.1 Score=48.68 Aligned_cols=38 Identities=26% Similarity=0.419 Sum_probs=34.7
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCeEEecC
Q 009173 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (541)
Q Consensus 186 ~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~ 223 (541)
-...+.||.+.++.+|||+|.+|++|.++.|.+|.|..
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 35568899999999999999999999999999999974
No 119
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=74.94 E-value=1.9 Score=46.87 Aligned_cols=37 Identities=27% Similarity=0.420 Sum_probs=34.4
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
...-+.||..+++.||||+|.+|++|.+..|-+|.|.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 4567889999999999999999999999999999996
No 120
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=74.27 E-value=4.4 Score=41.25 Aligned_cols=51 Identities=20% Similarity=0.331 Sum_probs=45.7
Q ss_pred ccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHHHHHHHHHHHHHhhc
Q 009173 290 GCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (541)
Q Consensus 290 G~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~V~~A~~lI~~~l~e 351 (541)
-++||.+|.|++.|+-.|.|.|-|.+ ..|.+.|....++.+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-----------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-----------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 68999999999999999999999953 3799999999999999999988863
No 121
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=74.15 E-value=3.9 Score=34.09 Aligned_cols=36 Identities=25% Similarity=0.376 Sum_probs=29.2
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEE
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIV 504 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I 504 (541)
...+|.|-...-|.|||++|++|++|++.-.....+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 346888888899999999999999998876554444
No 122
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=74.15 E-value=5.7 Score=39.76 Aligned_cols=59 Identities=17% Similarity=0.289 Sum_probs=45.2
Q ss_pred EEEEecccccccccccccchhhhhhcccCeeEEEccCcccccCCCCCceEEEEcCHHH-HHHHHHHHHHH
Q 009173 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK-VKDAVYNVTGR 348 (541)
Q Consensus 280 ~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d~~P~~~~s~ervVtItGt~e~-V~~A~~lI~~~ 348 (541)
.-+.|+...|-++||++|+.++-+.++++|+|.+-. +..|=|.|..+. ...|...|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~----------NG~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ----------NGRIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec----------CCEEEecCCCcchHHHHHHHHHHH
Confidence 456799999999999999999999999999999942 346777777773 44444444443
No 123
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=72.72 E-value=3.5 Score=36.25 Aligned_cols=31 Identities=26% Similarity=0.397 Sum_probs=26.3
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCC
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa 217 (541)
.+++.+-...-|.|||++|+.|++|++....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 4667778888999999999999999987643
No 124
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=72.52 E-value=3.7 Score=43.84 Aligned_cols=37 Identities=19% Similarity=0.412 Sum_probs=35.0
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEe
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~ 505 (541)
....+.||.+..+..|||+|.|++..++.||.+|.|.
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK 339 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence 4679999999999999999999999999999999996
No 125
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=71.20 E-value=5.4 Score=36.92 Aligned_cols=38 Identities=29% Similarity=0.347 Sum_probs=33.9
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
.+.+|.|-..+-|.|||++|.++++|...||-.-.|-.
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 35688898999999999999999999999999877763
No 126
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=68.89 E-value=5.3 Score=33.40 Aligned_cols=28 Identities=36% Similarity=0.529 Sum_probs=23.2
Q ss_pred EEEEeccccccceeccCchHHHHHHHHh
Q 009173 188 FRILCSNDKVGAVIGKGGTIIRALQSEA 215 (541)
Q Consensus 188 ~rilvP~~~vG~IIGKgG~~Ik~Iq~eT 215 (541)
.++.+-...-|.+||++|+.|++|++.-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 4555566888999999999999998875
No 127
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=66.45 E-value=7 Score=37.11 Aligned_cols=36 Identities=28% Similarity=0.249 Sum_probs=30.8
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
..-+.|-... |.-|||+|.+|+.+++..|-+|.|-+
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 4566666666 99999999999999999999999964
No 128
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=66.07 E-value=5 Score=43.70 Aligned_cols=38 Identities=18% Similarity=0.441 Sum_probs=35.0
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
....+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 35689999999999999999999999999999999963
No 129
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=65.64 E-value=5.3 Score=39.80 Aligned_cols=32 Identities=31% Similarity=0.413 Sum_probs=27.2
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhC
Q 009173 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (541)
Q Consensus 185 ~~~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTG 216 (541)
....++.|-...-|.||||+|+.|++|++...
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 34677888999999999999999999887653
No 130
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=63.99 E-value=11 Score=41.56 Aligned_cols=94 Identities=18% Similarity=0.408 Sum_probs=62.6
Q ss_pred ceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcc--cccCCCCCCCCCc
Q 009173 199 AVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT--SEKGLDFSSNKGL 276 (541)
Q Consensus 199 ~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~--~~~g~~~~~~~~~ 276 (541)
.++-+.|..||+|-++..-+|.|.... . + +++..+|...|.+ ++... ..+ ..|.
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP-s-----v-----------l~~~e~A~~~I~e-ivP~ea~i~~-i~Fd----- 97 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP-S-----V-----------LKPPEEARKIILE-IVPEEAGITD-IYFD----- 97 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc-h-----h-----------cCCHHHHHHHHHH-hCccccCcee-EEec-----
Confidence 456788999999999999888886321 0 0 1113345544443 33211 111 1111
Q ss_pred eeEEEEEecccccccccccccchhhhhhcccCeeEEEccC
Q 009173 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD 316 (541)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d 316 (541)
..+-++.|-...=|.+|||+|++.++|..+||-.-+|.+.
T Consensus 98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 1245788889999999999999999999999988888643
No 131
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=62.72 E-value=8 Score=32.33 Aligned_cols=28 Identities=29% Similarity=0.425 Sum_probs=22.6
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHh
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQIS 498 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~S 498 (541)
.++.|-...-|.+||++|.+|++|++.-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 4555556788999999999999987764
No 132
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=62.57 E-value=6.7 Score=34.46 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=24.6
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHhC
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQISG 499 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SG 499 (541)
.+|.|-...-|.|||++|++|++|++...
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 57777788899999999999999987654
No 133
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=58.13 E-value=9.1 Score=38.20 Aligned_cols=35 Identities=29% Similarity=0.494 Sum_probs=27.7
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHh----HhCC-EEEE
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQ----ISGA-KVIV 504 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq----~SGA-~I~I 504 (541)
.++|.|-...-|.|||++|++|++|++ .+|. .++|
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I 91 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI 91 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence 468888889999999999999998865 5565 3444
No 134
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=50.72 E-value=30 Score=39.77 Aligned_cols=94 Identities=17% Similarity=0.381 Sum_probs=60.6
Q ss_pred eeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEEecCCCCCCCCCHHHHHHHHHHHHHhhcccc-cCCCCCCCCCcee
Q 009173 200 VIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE-KGLDFSSNKGLLV 278 (541)
Q Consensus 200 IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~ItG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~-~g~~~~~~~~~~v 278 (541)
.+=+.|..||+|-++-.-+|.|-... . +.- +-.+|...|. +++....+ ....|. ..
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~-~-------~~~---------~~~~~~~~i~-~~~~~~~~~~~~~f~-----~~ 93 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDP-S-------VLL---------PPEEAIEKIK-EIVPEEAGITDIYFD-----DV 93 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecCh-h-------hcC---------CHHHHHHHHH-HhCCCcCCceeEEec-----CC
Confidence 45567899999999998888875310 0 001 1223443333 34422211 111121 12
Q ss_pred EEEEEecccccccccccccchhhhhhcccCeeEEEccC
Q 009173 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD 316 (541)
Q Consensus 279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d 316 (541)
+-++.|-...-|.+|||+|.++++|..+||-.-+|.+.
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 45788888999999999999999999999999888743
No 135
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=44.72 E-value=23 Score=35.83 Aligned_cols=30 Identities=20% Similarity=0.201 Sum_probs=23.7
Q ss_pred eEEEEEeccCcc-cceeeCCcchHHHHHhHh
Q 009173 469 TTVEIIVPENVI-GSVYGENGSNLLRLRQIS 498 (541)
Q Consensus 469 ~t~~V~IP~~~v-G~IIGkgGs~Ik~Irq~S 498 (541)
....|.|..+.. +-|||++|+.||+|...+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 556788887555 999999999999876554
No 136
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=43.03 E-value=25 Score=38.91 Aligned_cols=66 Identities=12% Similarity=0.149 Sum_probs=48.4
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEecCC--CCCCC-cceEEEecCCCCCCCCCHHHHHH
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECD-ERLITVTASEGPESRYSPAQKAV 252 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I~~~--~~~~~-eRvV~ItG~~~~~~~~s~a~~Ai 252 (541)
.+.+.||...+-.|||.||..|.+...+.++.|++... .+.+. ...|.|.....+.+.++-+-..+
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~ 518 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDK 518 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccH
Confidence 45689999999999999999999999999999998754 23232 23488888766655444333333
No 137
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=41.01 E-value=28 Score=38.62 Aligned_cols=38 Identities=26% Similarity=0.329 Sum_probs=33.5
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
.+.+|.|-..+=|.||||+|++.++|.+.+|-.-+|-.
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 45688999999999999999999999999998777753
No 138
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=40.99 E-value=15 Score=40.59 Aligned_cols=129 Identities=9% Similarity=0.038 Sum_probs=75.3
Q ss_pred cceeccCchHHHHHHHHhCCeEEecCCCCCCCcceEEE-ecCCCCCCCCCHHHHHHHHHHHHHhhcccccCCCCCCCCCc
Q 009173 198 GAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITV-TASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGL 276 (541)
Q Consensus 198 G~IIGKgG~~Ik~Iq~eTGa~I~I~~~~~~~~eRvV~I-tG~~~~~~~~s~a~~Ai~~i~~~i~e~~~~~g~~~~~~~~~ 276 (541)
-.+=||+--.+.+|++...|.+++.=. ...+.++.+. .|.. + ..+ +-+. +..+.+
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~-~~~gs~~~~~~~g~~-~------~F~---k~~~-~~~~EF------------ 447 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIV-SSTGSIVETNGIGEK-M------SFS---KKLS-IPPTEF------------ 447 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEE-ecCCcEEEEeccCcc-h------hhH---HHhc-CCcccC------------
Confidence 377888877799999999998654411 1122244332 3321 1 222 1111 111111
Q ss_pred eeEEEEEecccccccccccccchhhhhhcccCeeEEEccC-cccccCCCCCceEEEEcCHH---HHHHHHHHHHHHhhcc
Q 009173 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD-QLLKCISENDRVVQISGEFS---KVKDAVYNVTGRLRDN 352 (541)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I~~d-~~P~~~~s~ervVtItGt~e---~V~~A~~lI~~~l~e~ 352 (541)
.....+.||...+-.|||-||..|++++.+.++.|++... ..|..+ -. .-|.|.-... ++.-++--+.+++.++
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~-~~-dNV~I~~PrKn~~ni~~~KNd~~~~V~~~ 525 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQ-WH-DNVLIEAPRKNQDNISGKKNDKLDKVKQQ 525 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhh-hh-cceEEECCccCccchhcccccHHHHHhhh
Confidence 1245789999999999999999999999999999988732 233311 11 1255554433 3444444555566543
No 139
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=40.98 E-value=63 Score=34.28 Aligned_cols=50 Identities=22% Similarity=0.339 Sum_probs=43.7
Q ss_pred cCcccceeeCCcchHHHHHhHhCCEEEEeCCCCCCCccEEEEEeCHHHHHHHHHHHH
Q 009173 477 ENVIGSVYGENGSNLLRLRQISGAKVIVHEPRLGSTDRIVVISGTPDETQAAQSLLQ 533 (541)
Q Consensus 477 ~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~p~~~s~~RiItIsGtpeqV~~Aq~LI~ 533 (541)
.+..-.+.|..|.+++.|.+..|++|... .+.++|+|+...++.|..+++
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r-------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR-------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC-------CceEEEEechHHHHHHHHHHh
Confidence 56778899999999999999999888762 367999999889999999888
No 140
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=40.95 E-value=29 Score=39.89 Aligned_cols=38 Identities=29% Similarity=0.337 Sum_probs=34.2
Q ss_pred eEEEEEeccCcccceeeCCcchHHHHHhHhCCEEEEeC
Q 009173 469 TTVEIIVPENVIGSVYGENGSNLLRLRQISGAKVIVHE 506 (541)
Q Consensus 469 ~t~~V~IP~~~vG~IIGkgGs~Ik~Irq~SGA~I~I~~ 506 (541)
.+.+|.|-..+-|.||||+|+++++|.+.+|-.-+|-.
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 45688999999999999999999999999999888864
No 141
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=40.86 E-value=18 Score=36.54 Aligned_cols=30 Identities=27% Similarity=0.454 Sum_probs=23.4
Q ss_pred eEEEEEeccc-cccceeccCchHHHHHHHHh
Q 009173 186 VSFRILCSND-KVGAVIGKGGTIIRALQSEA 215 (541)
Q Consensus 186 ~~~rilvP~~-~vG~IIGKgG~~Ik~Iq~eT 215 (541)
+...|+|..+ +-+.||||+|+.||+|..++
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 5666778654 57899999999999886654
No 142
>PRK15494 era GTPase Era; Provisional
Probab=38.15 E-value=32 Score=36.22 Aligned_cols=37 Identities=22% Similarity=0.325 Sum_probs=27.4
Q ss_pred eEEEEEeccCcc-cceeeCCcchHHHHHh--------HhCCEEEEe
Q 009173 469 TTVEIIVPENVI-GSVYGENGSNLLRLRQ--------ISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~v-G~IIGkgGs~Ik~Irq--------~SGA~I~I~ 505 (541)
....|.|..+.. +-|||++|+.||+|.. ..|++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 456778887655 8999999999997654 456666553
No 143
>PRK00089 era GTPase Era; Reviewed
Probab=37.93 E-value=34 Score=34.83 Aligned_cols=37 Identities=24% Similarity=0.443 Sum_probs=26.8
Q ss_pred eEEEEEeccCc-ccceeeCCcchHHHHHh--------HhCCEEEEe
Q 009173 469 TTVEIIVPENV-IGSVYGENGSNLLRLRQ--------ISGAKVIVH 505 (541)
Q Consensus 469 ~t~~V~IP~~~-vG~IIGkgGs~Ik~Irq--------~SGA~I~I~ 505 (541)
....|.|..+. -+-|||++|+.||+|.. ..|++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 45677777654 48899999999997654 456666654
No 144
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=37.64 E-value=32 Score=33.53 Aligned_cols=31 Identities=29% Similarity=0.543 Sum_probs=26.4
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCC
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa 217 (541)
..++.+-...-|.|||++|..|++|+++-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 4677888888999999999999999987643
No 145
>CHL00048 rps3 ribosomal protein S3
Probab=36.97 E-value=33 Score=33.98 Aligned_cols=30 Identities=17% Similarity=0.147 Sum_probs=25.6
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhC
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTG 216 (541)
..++.|-....|.|||++|+.|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 466777788889999999999999998764
No 146
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=36.27 E-value=34 Score=34.01 Aligned_cols=33 Identities=24% Similarity=0.288 Sum_probs=27.0
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeE
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I 219 (541)
..++.+-...-|.|||++|..|++|+++-.-.+
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 366777788889999999999999998875443
No 147
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=36.16 E-value=34 Score=33.63 Aligned_cols=31 Identities=35% Similarity=0.464 Sum_probs=25.1
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCe
Q 009173 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAF 218 (541)
Q Consensus 188 ~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~ 218 (541)
.++.+-...-|.+||++|++|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 4455555888999999999999999987543
No 148
>PRK00089 era GTPase Era; Reviewed
Probab=36.10 E-value=24 Score=35.98 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=26.2
Q ss_pred eEEEEEecc-ccccceeccCchHHHHHHHH--------hCCeEEec
Q 009173 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSE--------AGAFISVG 222 (541)
Q Consensus 186 ~~~rilvP~-~~vG~IIGKgG~~Ik~Iq~e--------TGa~I~I~ 222 (541)
+...|+|.. +.-+.||||+|++||+|..+ .|++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 455567754 45788999999999987654 46665553
No 149
>COG1159 Era GTPase [General function prediction only]
Probab=35.34 E-value=40 Score=35.03 Aligned_cols=36 Identities=25% Similarity=0.412 Sum_probs=26.1
Q ss_pred eEEEEEeccC-cccceeeCCcchHHHHHhH--------hCCEEEE
Q 009173 469 TTVEIIVPEN-VIGSVYGENGSNLLRLRQI--------SGAKVIV 504 (541)
Q Consensus 469 ~t~~V~IP~~-~vG~IIGkgGs~Ik~Irq~--------SGA~I~I 504 (541)
....|.|+.+ .-|-||||+|+.||+|-.. .|++|.+
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 4456778775 4499999999999977544 4566555
No 150
>PRK15494 era GTPase Era; Provisional
Probab=32.12 E-value=30 Score=36.50 Aligned_cols=36 Identities=19% Similarity=0.376 Sum_probs=26.4
Q ss_pred eEEEEEeccc-cccceeccCchHHHHHHHH--------hCCeEEe
Q 009173 186 VSFRILCSND-KVGAVIGKGGTIIRALQSE--------AGAFISV 221 (541)
Q Consensus 186 ~~~rilvP~~-~vG~IIGKgG~~Ik~Iq~e--------TGa~I~I 221 (541)
+...|+|..+ .-+.||||+|+.||+|..+ .|++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 4566778654 5788999999999987554 4555554
No 151
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=31.52 E-value=44 Score=32.89 Aligned_cols=29 Identities=28% Similarity=0.386 Sum_probs=23.3
Q ss_pred EEEEeccCcccceeeCCcchHHHHHhHhC
Q 009173 471 VEIIVPENVIGSVYGENGSNLLRLRQISG 499 (541)
Q Consensus 471 ~~V~IP~~~vG~IIGkgGs~Ik~Irq~SG 499 (541)
.++.|-...-|.+||++|++|+++++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 45555557889999999999999887664
No 152
>COG1159 Era GTPase [General function prediction only]
Probab=30.99 E-value=34 Score=35.48 Aligned_cols=37 Identities=22% Similarity=0.466 Sum_probs=26.0
Q ss_pred ceEEEEEecc-ccccceeccCchHHHHHHH--------HhCCeEEe
Q 009173 185 EVSFRILCSN-DKVGAVIGKGGTIIRALQS--------EAGAFISV 221 (541)
Q Consensus 185 ~~~~rilvP~-~~vG~IIGKgG~~Ik~Iq~--------eTGa~I~I 221 (541)
.+...|+|+. ++-|.||||+|+.||+|-. -.+++|.+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 3445567764 4579999999999998754 44666554
No 153
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=30.67 E-value=50 Score=32.26 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=24.4
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHh
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQIS 498 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~S 498 (541)
..+|.|-...-|.|||++|.+|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46777878888999999999999887654
No 154
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=30.14 E-value=38 Score=33.30 Aligned_cols=35 Identities=26% Similarity=0.416 Sum_probs=27.8
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCeEEe
Q 009173 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (541)
Q Consensus 187 ~~rilvP~~~vG~IIGKgG~~Ik~Iq~eTGa~I~I 221 (541)
.+.+-+-.+..|.+|||.|.++..||--+.+-+.-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 44455566669999999999999999988765554
No 155
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=28.46 E-value=53 Score=32.69 Aligned_cols=29 Identities=24% Similarity=0.422 Sum_probs=24.0
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHh
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQIS 498 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~S 498 (541)
..+|.|-...-|.|||++|..|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 35777777888999999999999887654
No 156
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=27.45 E-value=36 Score=28.55 Aligned_cols=33 Identities=30% Similarity=0.273 Sum_probs=26.7
Q ss_pred chHHHhhhhcccCccccccccccchHHHHHHhhhcCc
Q 009173 59 SHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGP 95 (541)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 95 (541)
.|-.|-.-|++||.||.-.|| .|+|+|.+|++-
T Consensus 16 ~~~~iF~FL~~~P~GT~~~~i----R~~L~rYI~~~G 48 (97)
T PRK13916 16 DYPQIFDFLENVPRGTKTAHI----REALRRYIEEIG 48 (97)
T ss_pred ccHHHHHHHHHCCCCCccHHH----HHHHHHHHHhcC
Confidence 466778889999999988776 578888888763
No 157
>CHL00048 rps3 ribosomal protein S3
Probab=27.43 E-value=56 Score=32.33 Aligned_cols=29 Identities=10% Similarity=0.147 Sum_probs=24.1
Q ss_pred EEEEEeccCcccceeeCCcchHHHHHhHh
Q 009173 470 TVEIIVPENVIGSVYGENGSNLLRLRQIS 498 (541)
Q Consensus 470 t~~V~IP~~~vG~IIGkgGs~Ik~Irq~S 498 (541)
..+|.|-...-|.|||++|.+|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 45677777788999999999999988765
No 158
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=27.01 E-value=55 Score=34.37 Aligned_cols=33 Identities=24% Similarity=0.517 Sum_probs=26.4
Q ss_pred CceEEEEEecccc-ccceeccCchHHHHHHHHhC
Q 009173 184 QEVSFRILCSNDK-VGAVIGKGGTIIRALQSEAG 216 (541)
Q Consensus 184 ~~~~~rilvP~~~-vG~IIGKgG~~Ik~Iq~eTG 216 (541)
-.+..+++||... .-.||||||..|++|-.+.+
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3467789999875 55689999999999987654
No 159
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=26.40 E-value=45 Score=32.81 Aligned_cols=35 Identities=14% Similarity=0.348 Sum_probs=28.5
Q ss_pred EEEEEecccccccccccccchhhhhhcccCeeEEE
Q 009173 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (541)
Q Consensus 279 t~~l~VP~~~vG~IIGKgG~tIkeIr~~TGA~I~I 313 (541)
++.+.|-.+..|.||||.|+++..||-.+.+-+.-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 56677788889999999999999999887664433
No 160
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=26.36 E-value=60 Score=34.11 Aligned_cols=32 Identities=19% Similarity=0.375 Sum_probs=25.5
Q ss_pred ceEEEEEeccCcc-cceeeCCcchHHHHHhHhC
Q 009173 468 NTTVEIIVPENVI-GSVYGENGSNLLRLRQISG 499 (541)
Q Consensus 468 ~~t~~V~IP~~~v-G~IIGkgGs~Ik~Irq~SG 499 (541)
.+..++.||...- ..+|||||..|++|-+..+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3678999998654 6789999999998866543
No 161
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=24.10 E-value=1.6e+02 Score=22.78 Aligned_cols=45 Identities=20% Similarity=0.505 Sum_probs=30.9
Q ss_pred cchHHH--HHhHhCCEEE-Ee------CCCCCC---CccEEEEEeCHHHHHHHHHHH
Q 009173 488 GSNLLR--LRQISGAKVI-VH------EPRLGS---TDRIVVISGTPDETQAAQSLL 532 (541)
Q Consensus 488 Gs~Ik~--Irq~SGA~I~-I~------~p~~~s---~~RiItIsGtpeqV~~Aq~LI 532 (541)
|.+|++ +++.+|+.|. |. .|.+++ ....+.|.|++++++++..++
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHhh
Confidence 557888 7787788743 22 233333 467899999999999988764
No 162
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=23.68 E-value=2.2e+02 Score=23.67 Aligned_cols=51 Identities=16% Similarity=0.052 Sum_probs=41.2
Q ss_pred CcchHHHHHhHhCCEEEEeCCCC---CCCccEEEEEeCHHHHHHHHHHHHHHHh
Q 009173 487 NGSNLLRLRQISGAKVIVHEPRL---GSTDRIVVISGTPDETQAAQSLLQAFIL 537 (541)
Q Consensus 487 gGs~Ik~Irq~SGA~I~I~~p~~---~s~~RiItIsGtpeqV~~Aq~LI~~~I~ 537 (541)
|=.-+.++=+..|++++...+.. ...+.+++|+|+..++..|...+++++.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 44578888888899998874433 2367999999999999999999999885
No 163
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.24 E-value=77 Score=31.27 Aligned_cols=29 Identities=31% Similarity=0.515 Sum_probs=24.7
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhC
Q 009173 188 FRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (541)
Q Consensus 188 ~rilvP~~~vG~IIGKgG~~Ik~Iq~eTG 216 (541)
+++.+-...-|.|||++|..|++|++.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 66777888889999999999999997653
Done!